In order to solve the problem of significant nitrate accumulation during the process of factorycirculating aquaculture, which affects the growth and development of aquaculture species, this project added a solid-phase denitrification (SPD) treatment unit to the recirculating aquaculture system (RAS) to explore the removal effect of the treatment unit on nitrate in the aquaculture water and the change of the microbial community structure of each unit in the RAS before and after the setting of the SPD unit. The results showed that the SPD treatment unit can remove nitrate accumulated by RAS to approximately 40 mg/L after 100 days of operation, with a nitrate removal rate of 0.32 g/(L·d). The analysis of microbial community structure showed that in each unit of the RAS, Proteobacteria, Bacteroidetes, and Cyanobacteria were all dominant phyla before and after the setting of SPD units, although their abundance changed. Experiments have proved that setting up an SPD treatment unit in the RAS can better purify the nitrate pollution accumulated in the system, which provides certain theoretical reference and technical support for its large-scale practical application.