The microbial structure and metabolic potential, particularly with regard to nitrogen (N) cycling, in integrated multitrophic aquaculture (IMTA) ponds with shrimp remain unclear. In this study, an analysis of microbial community taxonomic diversity and a metagenomic analysis of N-related genes were performed in a shrimp-crab pond (Penaeus japonicus-Portunus trituberculatus, SC) and a shrimp-crab-clam pond (P. japonicus-P. trituberculatus-Sinonovacula constricta, SCC) to evaluate microbial structure and N transformation capacities in these two shrimp IMTA ponds. The composition of the microbial communities was similar between SC and SCC, but the water and sediments shared few common members in either pond. The relative abundances of N cycling genes were significantly higher in sediment than in water in both SC and SCC, except for assimilatory nitrate reduction genes. The main drivers of the differences in the relative abundances of N cycling genes in SC and SCC were salinity and pH in water and the NO2- and NH4+ contents of pore water in sediment. These results indicate that the coculture of S. constricta in a shrimp-crab pond may result in decreased N cycling in sediment. The reduced N flux in the shrimp IMTA ponds primarily originates within the sediment, except for assimilatory nitrate reduction.