Studies on food supply values, the basis of eco-service values, and their factors of different pond aquaculture ecosystems are helpful to explain the influences of the inputted factors and their variations among these ecosystems and provide information for stakeholders to adjust their decisions and behaviors to increase their total eco-service values. On the basis of continued records from 2011 to 2012 of 18 ponds of three pond aquaculture ecosystems, namely Litopenaeus vannamei, Macrobrachium nippponensis and carp fresh water pond aquaculture ecosystems in Qingpu, Fengxian, and Jiading, three suburban districts of Shang, this paper analyzed the costs, returns, net food supply values and their regional and temporal fluctuations. The results showed that: (1) the net food supply values of the three ecosystems are 143252.4, 135883.7, and 52623.1Yuan/Ha in 2011 correspondently, with the Litopenaeus vannamei pond aquaculture ecosystem (LVPAE) ranking highest and the carp pond aquaculture ecosystem (CPAE) lowest among them, and the trend was same in 2012, but the values decreased than that of 2011 with the rate of 30.0%( LVPAE), 38.0 %( Macrobrachium nippponensis pond aquaculture ecosystem, MNPAE) and 13.7 %( CPAE). (2)The dominant factors of the net food supply values of these ecosystems are the produce price and variable costs; fry and feed costs are the main variable factors producing the noticeable difference among the ecosystems. (3) The cost-benefit ratio of per unit product of the CPAE, LVPAE and MNPAE changed from 27.5%,91.7%,129.0% in 2011 to 23.0%,73.8% and 63.8% in 2012, with the CPAE ranked lowest among them in both years.(4) For all the three ecosystems, their net food supply values may not always change in same trends with their net eco-service values, if stakeholders want to keep an balance between these two types of values, MNPAE should be encouraged in these districts.