The structure and trophic relationship of food webs are fundamental research topics in modern ecology. Food webs are important for the understanding of patterns and processes of an ecosystem. Inventory of the stable isotopes of carbon and nitrogen in organisms has been increasingly used as a powerful approach to study the structure and dynamics of food webs and trophic relationships in the studies in a wide variety of ecosystems. Carbon isotope ratios (δ13C) are used to trace food sources of consumers, while nitrogen isotope ratios (δ15N) are mainly used to quantify trophic levels of organisms. By using stable isotopes analysis, the food web structures and trophic relationships of multiple species coexisted in different farming systems: (1) rice-fish culture（R-F）; (2) rice-fish-duck culture（R-F-D）were examined in this paper. The results showed that a weak positive relativity existed between the δ13C and δ15N values and the body length and weight of fishes. Compared with the δ13C and δ15N values in Anas platyrhynchos domestic wing muscles, the ones in leg muscles were not different, while the ones in livers were significantly different. The δ13C values of sedimentary organic matter (SOM)showed no difference between R-F and R-F-D. The δ13C values of particulate organic matter (POM) in R-F ((-27.4±0.8) ‰) lower than that in R-F-D（(-26.7±0.5) ‰). The δ13C values of macrophytes in R-F ranged from -31.9‰―-26.1‰, and were not significantly different from that in R-F-D (-31.3‰―-28.5‰). The δ13C was significantly higher in the submersed macrophytes than that in other macrophytes, while the δ15N was significantly higher in the emergent macrophytes than that in other macrophytes. The similar δ13C values in Spirogyra spp. and fish indicated that phytoplankton was the major food source for the fish. The similar δ13C values in Anodonta spp, Macrobrachium spp. zooplankton, SOM and POM indicated that POM and demersal algae were the major food source for the most zooplankton and zoobenthos. The δ15N values indicated that Anas platyrhynchos domestic was at the highest trophic level. The δ15N values in fish under R-F were similar to that in fish under R-F-D. This indicated adding ducks had little effects on the major food source for fish. The δ15N values of POM in R-F，(-4.4±1.1)‰ were significantly lower than that in R-F-D (-3.5±0.6)‰. The δ15N values of macrophytes in R-F ranged from 0.8‰―5.6‰ and were not significantly different from that in R-F-D (0.5―5.2)‰. According to the calculation of δ15N values，the relative trophic levels of both zooplankton and fish in R-F，were higher than that in R-F-D. Compared with R-F, the relative trophic levels of fish in R-F-D decreased.