At present, academics on the ecological services value research focus on the positive aspects, while the negative service values, such as environment cost, is received little attention. Pond aquaculture performs multiple functions, including aquatic products supply, air quality adjustment as well as culture service and so forth. As a kind of special ecological system, the pond aquaculture also has the environment cost in its production process. A clear cognition of the positive and negative ecological services values in pond aquaculture will be a great significance to avoid the blindness and short-term version in the process of production, keep the development of pond aquaculture sustainable and promote the development of aquaculture in harmony with the environment protection. This paper firstly adopts double-bounded dichotomous contingent valuation method (CVM) and random cluster sampling method to attain the local residents' willing to accept (WTA), 354 questionnaires were sent out and 340 effective questionnaires were returned, the effective response rate was therefore 96.05%. Then the paper adopt Logit and Biprobit regression models of econometrics and STATA10.0 software was utilized for analyzing the environment cost of pond aquaculture in the DianShan Lake, Shanghai. Through these methods adopted, the paper has summarized these results as following: 1) The ecological compensation E(WTA) standard of Shanghai residents for the environment pollution damage is 104.89 RMB Yuan per person in Logit model and 121.89 RMB Yuan per person in Biprobit model; 2) In 2010, the total pond aquaculture environment cost is about 19.8226 million Yuan, namely 5105 RMB Yuan·a^-1·hm^-2); 3) The latest research released that several economic social factors such as the income of the household, education background and age lay a great influences on residents' willingness to accept the ecological compensation, but these factors will cause no strict trend influences on the residents' WTA at present. Such as the income of the household, education background of residents affect the E (WTA), which shows a positive effect on the relationship of E (WTA) standard. The 18-45 years old residents pay more attention to the environmental protection. If government takes the ecological compensation policy, they may be the main stakeholders. The paper also mentions the discussions: 1) Because these social economic factors have common influences on the E (WTA) standard of residents, but the size and direction of these influences are not absolute, it needs to do a further study based on the actual situation to establish a stable structure model to determine the size and direction of these influences; 2) By the LR and WALD test, the research indicates that the double-bounded dichotomous discrete CVM has a stronger stability than the single-bounded dichotomous discrete CVM, thus the double-bounded dichotomous discrete CVM can become a relatively stable research method for ecological system service value study; 3) The environment property right should be the applicable standard to WTA and WTP. Meanwhile, improving the questionnaire design accuracy, adjusting the research course etc can overcome the differences between WTA and WTP effectively; 4) Government should make and conduct a make-up policy for ecological compensation according to the real situation in order to achieve the environmental equity and sustainable development.