As one of effective means to balance ecological and economic development, ecological payment has attracted wide attention of scholars, but few studies in this field have been conducted from such microeconomic perspectives as farmers' (fish farmers') property and willingness to participation. On the basis of data from field survey in Qingpu, Jiading, Fengxian and Nanhui Districts in Shanghai, 127 pond farmers’ willingness to participate in ecological payment and their influencing factors were analyzed by ordinal Logit regression model. The results show that : (1) 88.98% of the pond farmers are willing to participate in ecologically payment; (2) Willingness to participate is positively impacted by educational level, breeding pond areas, aquatic produce value, household assets, household per capita income, degree of trust among persons around them and the number of relatives in the village; this willingness is negatively affected by such factors as household arable land areas,the opportunity to get loan, family member working in government or not, joining in cooperative associations or not; (3) Willingness to participate in this arrangement is positively correlated with human capital, physical capital, financial capital, and social capital,and regression coefficients between them are 2.677, 1.153, 2.635, 2.766 respectively, occurrence ratio (Expβ) are 14.514, 3.168, 13.943, 15.895 respectively; it is negatively affected by natural capital, the regression coefficient is -0.602, and occurrence ratio is 0.548.According to these results, it is proposed to conduct training of farmers, improve fisheries insurance and social credit system, upgrade traditional industries to improve the livelihoods capital levels of farmers so as to increase the level of willingness to participate in aquaculture eco-payment in Shanghai.