Aquatic litter decomposition is highly dependent on contributions and interactions at different trophic levels. The invasion of alien aquatic organisms like the channeled apple snail (Pomacea canaliculata) might lead to changes in the decomposition process through new species interactions in the invaded wetland. However, it is not clear how aquatic macroinvertebrate predators like the Chinese mitten crab (Eriocheir sinensis) will affect the nutrient cycle in freshwater ecosystems in the face of new benthic invasion. We used the litter bag method to explore the top-down effect of crabs on the freshwater nutrient cycle with the help of soil zymography (a technology previously used in terrestrial ecosystems). The results showed significant feeding effects of crabs and snails on lotus leaf litter and cotton strips. Crabs significantly inhibited the intake of lotus litter and cotton strips and the ability to transform the environment of snails by predation. Crabs promoted the decomposition of various litter substrates by affecting the microbial community structure in the sediment. These results suggest that arthropod predators increase the complexity of detrital food webs through direct and indirect interactions, and consequently have an important impact on the material cycle and stability of freshwater ecosystems. This top-down effect makes macrobenthos play a key role in the biological control and engineering construction of freshwater ecosystems.