The Chinese mitten crab (CMC) is an economically important species that consumers prefer mainly because of its delightful taste and aroma. The taste of CMC varies depending on its environmental conditions. Consumers prefer lake-sourced crabs to pond-cultured ones, but the production of crabs in lakes is greatly discouraged because of its adverse impacts on the local ecosystem. This study investigates the dynamics of the food web structure and trophic levels (TL) of both lake and pond ecosystems to apply the knowledge of the lake-cultured system to pond-cultured production using the stable isotope ratios of C and N. Furthermore, the TL was estimated and the IsoSource model was used for diet contribution estimates. The results show that the δ13C of the crab in the pond ecosystem (− 22.6 ± 0.3‰) was more enriched than that in the lake ecosystem (− 25.7 ± 0.4‰) indicating a clear distinction (P < 0.05) which is mainly influenced by their diet. The δ15N of the crab obtained from the lake ecosystem was higher (10.6 ± 0.1‰) than that in the pond ecosystem (8.6 ± 0.2‰), which is indicative of the nutritive value of the lake-culture crabs and consumers’ preference for this type. However, 15N compositions of the lake- and pond-cultured crabs did not differ significantly (P > 0.05), suggesting a similar TL. The crabs also occupied higher TL in both ecosystems under consideration, indicating a reliance of crab on the animal matter for food. This study provides more insights for all concerned stakeholders to make an informed decision with respect to the production and consumption of CMC.