The crab-rice comprehensive breeding model provides a new model for aquaculture and agriculture to change from single management to integrate management in China. In order to promote the popularization of crab-rice co-cropping model, a study was conducted to assess the nutritional structure and energy flow in a system using the ecopath ecological channel model. The results of the study showed that the highest nutrient level of crab-rice co-cropping ecosystem (3.140) was higher compared to that of rice monoculture system (2.676), there are two main ways of energy flow in an ecosystem, namely, the herding and feeding chain with submerged plants and other microtubule plants as the starting point, and the saprophytic chain with detritus as the starting point; rice and crab were used as farmland ecosystem experimental groups in June and October FCI(0.55 and 1) and FCL (2.066 and 2.077). The FCI (1.14 and 0.81) and FCL (2.089 and 2.137) of rice cropping farmland ecosystem control group in June and October showed that the rice-crab joint model can form a stable ecosystem. Besides, Eriocheir sinensis could promote the energy flow of the complete ecosystem, and the system maturity increased with the growth of the crab. The maturity of rice-crab co-cropping farmland ecosystem was lower than that of monoculture system, which indicated that the maturity of rice-crab co-cropping system was more space in the rice co-cropping ecosystem. The connection index of rice and crab farming ecosystem in June and October was 0.135 and 0.135 respectively. In the same months, the link index of rice field monoculture system was 0.188 and 0.161, respectively. The link strength between the functional groups of the co-cropping system was weaker than that of the monoculture system, and the degree of stability was relatively low. The primary productivity of rice-crop farming ecosystem was significantly higher than that of single-cropping farmland ecosystem, and the development of rice-shrimp farming ecosystem was better.