1.王霞, 方文东,陈荣裕 (2018): 南海北部海面高度的季节内变异及其传播特征.热带海洋学报 (in press).
2. Wang X., W. Fang, R. Chen, et al.(2017): The summer-fall anticyclonic eddy west of Luzon: Structure and evolution in 2012 and interannual variability. Journal of Marine Systems. 172, 84-92.
3. Qiu F., W. Fang, A. Pan, et al. (2016): Interannual to decadal variation of spring sea level anomaly in the western South China Sea. Chin. J. Ocean. Limnol. doi:10.1007/s00343-016-5203-1.
4. Xiang R., W. Fang, S. Zhou (2016): The anticyclonic circulation in the southern South China Sea: Observed structure, seasonal development and interannual variability. Journal of Marine Systems. 154, 131-145.
5. 向荣, 方文东,鲁远征,黄孝荣,周生启 (2015): 2014年9月南海西部冷涡及东向急流三维结构观测. 热带海洋学报,34 (6): 1-10.
6. 丘福文, 方文东, 朱大勇, 查晶 (2015): 2005-2010年南海海平面异常升高的特征与机制.热带海洋学报,34 (5): 11-18.
7. Fang W., P. Guo, C. Liu, G. Fang, S. Li (2015): Observed sub-inertial current variability and volume transport over the continental shelf in the northern South China Sea. Estuarine, Coastal and Shelf Science. 157, 19-31.
8. Fang, W., F. Qiu and P. Guo (2014): Summer circulation variability in the South China Sea during 2006–2010. Journal of Marine Systems 137,47-54.
9. Guo, P., W. Fang, C. Liu, and F. Qiu (2012): Seasonal characteristics of internal tides on the continental shelf in the northern South China Sea. J. Geophys. Res., doi:10.1029/2011JC007215.
10. Qiu, F., W. Fang, Y. Fang, and P. Guo (2012): Anomalous oceanic characteristics in the South China Sea associated with the large-scale forcing during 2006–2009, J. Mar. Syst.,doi:10.1016/j.jmarsys.2012.03.010.
11. Cai, Y., Guo P., Fang W. (2012): Internal tides in the northern South China Sea From 20-day insitu mooring observations in 1998, Marine Science Bulletin, 14(2),12-23.
12. Fang G., Wang G., Fang Y., Fang W. (2012): A review on the South China Sea western boundary current. Acta Oceanol. Sin., 31(5), 1-10, DOI: 10.1007/s13131-012-0231-y.
13. Qiu Fuwen, Fang Wendong, Fang Guohong (2011): Seasonal-to-interannual variability of chlorophyll in the Central Western South China Sea extracted from SeaWiFS. Chinese Journal of Oceanology and Liminology,29(1), 18-25.
14. 丘福文,方文东,郭朴(2011), 2000—2008年期间南海海面温度的年际与空间变异, 海洋学报, 33(3):11-18.
15. 丘福文, 方文东, 南海海面高度年际变化的S-EOF 分析. 热带海洋学报,2010,29 (4),8?13.
16. Qiu Fuwen, Fang Wendong (2010): interannual variability and spatial pattern of the sea surface temperature in the South China Sea during 2000-2008.(POSEC国际会议poster)
17.Xie X., G. Chen, X. Shang, and W. Fang (2008): Evolution of the semidiurnal (M2) internal tide on the continental slope of the northern South China Sea. Geophys. Res. Lett., 35, L13604, doi:10.1029/2008GL034179.
18. 陈荣裕,方文东,黄企洲(2007) 三亚湾水文物理环境概述。见:《三亚湾海洋生物资源与生态环境》,北京,科学出版社, pp266.
19. Fang, W., J. Guo, P. Shi, and Q. Mao (2006), Low frequency variability of South China Sea surface circulation from 11 years of satellite altimeter data, Geophys. Res. Lett., 33, L22612, doi:10.1029/2006GL027431.
20. Guo P., Fang W., Gan Z.,Chen R.(2006): Internal tide characteristics over northern South China Sea continental slope. Chinese Science Bulletin, 51(Supp. II),17-25. (通讯作者)
21. 郭朴,方文东,甘子钧,陈荣裕. 南海北部大陆坡区的内潮特征,科学通报,2006,51(Supp. II):15-22.
22. 郭朴,方文东,于红兵(2006): 近海陆架区内潮观测研究进展,地球科学进展,21(6):617-624.
23. 郭俊建, 方文东, 方国洪, 陈海英. 基于11年卫星高度计资料的南海表层环流时空变化,科学通报,2006, 51(Supp. II):1-8.
24. Guo J., Fang W., Fang G., Chen H.(2006): Variability of surface circulation in the South China Sea from satellite altimeter data. Chinese Science Bulletin, 51(Supp. II) ,1-8. (通讯作者)
25.. Fang W., Shi P., Long X.,Mao Q.(2005) : Internal solitons in the northern South China Sea from insitu observations. Chinese Science Bulletin, 50(15):1627-1631.
26..方文东,施 平,龙小敏,毛庆文(2005): 南海北部孤立内波的现场观测,科学通报,2005,50(14)1400-1404.
27.. Fang W, Shi P, Huang Q, Long X (2003),Basic Features of Vertical Structure of Upper Water Temperature and Salinity in the Northern South China Sea around the Summer Monsoon Onset. Acta Meteorologica Sinica, 17, Supplement, 262-272.
28.. Fang W, Fang G, Shi P, et al.(2002): Seasonal structures of upper-layer circulation in the southern South China Sea from in-situ observations. Journal of Geophysical Research, C(11): 2002JC001343.
29.. Fang W, Shi P, Huang Q, Long X (2002): Basic Features of Vertical Structure of Upper Water Temperature and Salinity in the Northern South China Sea around the Summer Monsoon Onset. Acta Meteorologica Sinica, 17, Supplement, 262-272
30. 方国洪,魏泽勋,黄企洲,方文东(2002): 南海南部与外海间的体积和热、盐输运及其对印尼贯穿流的贡献,海洋与湖沼,33(3):296-302.
31. 方文东,黄企洲,邱章,施平(2001): 南部春夏季季风转换期的异常表层水,热带海洋学报,20(1): 77-81.
32. 黄企洲,方文东, 陈荣裕 (2001): 南沙群岛海区西南季风变化与表层流结构和演变关系的探讨, 热带海洋, 20(1), 18-26.
33. Fang W, Shi P, Mao Q, Gan Z. (2000): Upper-ocean variations of the northern South China Sea from mooring station observations. Acta Oceanologica Sinica, 19(4),25-35.
34. 方文东(2000). 南海南部海洋环流的结构与季节变化. 中国科学院博士学位研究生论文, pp112.
35. 方文东,施平,毛庆文,甘子钧(2000): 南海北部上层海洋变化的定点观测分析,海洋学报,22(5),23-30.
36. 方文东, 陈荣裕,毛庆文 (2000): 南海北部内波引起的突变性海流, 热带海洋, 19(1): 70-74.
37. 方文东,郭忠信(2000): 1994年9月南沙海区表层水、次表层水温盐分布及其运动特征,南海海洋科学集刊,第13集,32-39.
38. 方文东,郭忠信,方国洪(2000): 冬季南海南部的陆架坡折锋,南海海洋科学集刊,第13 集,40-48.
39. 郭忠信,方文东, 陈福培等 (2000): 南沙海域环流及其主要海流, 南海海洋科学集刊,第13 集,1-25.
40. 邱章,方文东(2000): 南海北部斜压海流的垂向变化, 台湾海峡, 19(4),405-412.
41. Gao R, Zhou F, Fang W. (2000):SST intraseasonal oscillation and atmospheric forcing system of the South China Sea, Chinese Journal of Oceanology and limnology, 2000,18(4), 289-296.
42. 邱章,方文东(1999): 南海北部春季海流的垂向变化,热带海洋, 18(4): 32-38。
43. 方文东(1998): 南海南部海区夏季的环流结构,南海海洋科学集刊,第12 集, 217-213.
44. Fang W, Guo Z, Huang Y (1998): Observational study of the circulation in the southern South China Sea, Chinese Science Bulletin, 43(11): 898-905.
45. 方文东 (1998),两个显著性检验方法在海洋大数据量主成分分析中的应用,热带海洋, 3(4): 90-94.
46. 方文东, 方国洪(1998):南海南部海洋环流研究的新进展,地球科学进展, 13(2): 166-172.
47. 方文东,宋运发(1998): 海洋大数据序列时空变化主成分分析方法,热带海洋,17(3):10-17
48.Fang G. Fang W. et al. (1998): Circulation, internal tide and soliton in South China Sea, Collected papers of the Sino-US Marine Science & Technology Collaboration Workshop, August, Qingdao.
49. Fang G, Fang W, Fang Y et al. (1998): A survey of studies on the South China Sea upper circulation,Acta Oceanographica Taiwanica, 37 (1): 1-16.
50. 方文东,郭忠信,黄羽庭(1997): 南海南部海区的环流观测研究,科学通报, 42(21): 2264-2271.
51. 方文东(1996): 冬季南海南部陆架坡折锋及其动力学解释,南海研究与开发,第2期:12-22.
52. Fang W and Hsieh W,(1993): Summer sea surface temperature variability off Vancouver Island from satellite data, J. Geophys. Res., 1993, 98(C8): 14391-14400.
53. Fang Wendong (1993): Summer SST variability off Vancouver Island from Satellite data, 1984-91, Master's thesis, pp78, The University of British Columbia, Vancouver, Canada.
54. 郭忠信, 方文东.(1988): 1985年9月的吕宋海峡黑潮及其输送, .热带海洋,1988 (2).
其它论文:
1. 方文东(2002): 关于科研团队组建的一些认识,科技管理研究,22(4):42-43.
2. 方文东(2004): 对研究所创新文化的一些认识, 科技管理研究,24(3):49-50.
3. 中国科学院南海海洋研究所(2005): 国内首创的海洋观测开放平台------南海北部开放航次.
4. 方文东,李丽璇, 蔡艳雅(2007): 提高科研产出影响力的一些思考, 科学新闻杂志.
5. 方文东(2008): 提高国家创新能力 推动经济社会发展——对加拿大科技创新管理的几点认识. 科学新闻杂志.
6. 方文东(2011): 澳大利亚公共服务的一些特征及启示. 见: 中国科学院赴澳大利亚综合管理高级培训班论文集.