Integrated multi-trophic aquaculture (IMTA) has emerged as an ecological intensification strategy capable of enhancing nutrient utilization and improving environmental stability in mariculture systems, yet the microbial mechanisms driving nutrient transformations remain insufficiently understood. This study investigated how culture mode (IMTA vs. monoculture) shape water quality, sediment microbial communities, and nutrient cycling processes in a shrimp–sea urchin system by combining water-quality monitoring, nutrient analysis, 16S rRNA high-throughput sequencing, and redundancy analysis. IMTA significantly increased turbidity, chlorophyll-a, phosphate, ammonium, and nitrite compared with monoculture, while physico-chemical parameters remained stable. Sediment microbiota in IMTA exhibited substantially higher alpha diversity and showed a clear compositional separation from monoculture communities. At the genus level, IMTA sediments were enriched in Vibrio, Motilimonas, and Ruegeria, distinguishing them from monoculture systems. At the phylum level, IMTA was characterized by increased abundances of Proteobacteria and Bacteroidota, accompanied by a marked decline in Spirochaetota. Functional predictions indicated that microbial communities were predominantly characterized by pathways related to amino acid and carbohydrate metabolism, as well as nutrient remineralization. RDA and correlation analyses further identified turbidity, chlorophyll-a, phosphate, ammonium, and nitrite as the principal drivers of microbial divergence. Overall, the findings demonstrate that IMTA reshapes sediment microbial communities toward more efficient nutrient-processing assemblages, thereby promoting active nitrogen and phosphorus transformations and improving biogeochemical functioning relative to monoculture. These results provide mechanistic insight into how IMTA supports nutrient recycling and environmental sustainability in modern mariculture systems.