We determined the effect of Chinese mitten crab (CMC) pen culture on the quantified spatial distribution of the macrozoobenthic community and sediment nutrients in Lake Yangcheng. Redundancy analysis indicated that water temperature, macrophyte occurrence, sediment type, and crab culture were the main environmental factors that influence the spatiotemporal macrozoobenthic distribution. Macrozoobenthic assemblages in the lake were characterized by eutrophic indicator species. In the most polluted estuaries, the abundance and diversity indices of the whole community and abundance of chironomids and oligochaetes were significantly depressed, and sediment carbon (C) and phosphorus (P) were significantly enhanced compared with those in the western, middle (MB), and eastern basin (EB). Crab culture in this lake had significant effects on the species composition of the macrozoobenthic community in one of three CMC culture pens (CP), and generally depressed the abundance of most chironomid and oligochaete species. Significantly increased diversity, evenness, sediment carbon and nitrogen content, and sediment C:P ratio in the CP were found compared with those in the three basins. However, no conspicuous difference in sediment P content between the CP and the two basins of MB and EB was detected. Our results showed that the enhanced diversity and evenness of macrozoobenthos might be associated with the joint effect of macrophyte planting and crab predation, and macrophyte planting may modify the effects of CMC culture by leading to disproportional accumulation of C and N in the sediment relative to P in the CP of the lake.