Biofloc technology (BFT) is extensively used in the treatment of water quality in intensive shrimp aquaculture systems. However, the rapid accumulation of biofloc in middle-to-late culture stages poses challenges for system management, impacting the economic yield of aquaculture operations. To address this issue, an advanced biofloc system (A-BS) that integrates a moving bed biofilm reactor (MBBR) with BFT was constructed, and the biofloc system (BS) was used as a control group. During a 100-day pilot-scale operation, the A-BS group effectively regulated water quality and enhanced the growth rate of Pacific white shrimp (Litopenaeus vannamei). In the A-BS group, the average concentrations of ammonia, nitrite, chemical oxygen demand, and mixed liquor suspended solids were substantially reduced compared to those in the BS group, measuring 0.19, 0.55, 36.36, and 229 mg/L, respectively, across the middle-to-late culture stages. Notably, the final stocking density and survival rate of shrimp in the A-BS group, reached 7.04 kg/m3 and 81.22 %, surpassing those in the BFT group. Furthermore, microbial community and functional gene analyses revealed more in-depth insights into the related mechanisms. Bacterial abundance and diversity, as well as the presence of denitrification genes such as Unclassified_f_Rhodobacteraceae and Paracoccus, were markedly higher in the A-BS group than in the BS group. The integration of MBBR into A-BS significantly increased the abundance of amoA and nirK genes, which are crucial for water quality stability during later culture stages. This proof-of-concept investigation confirms that the MBBR–BFT coupling process in A-BS holds promise for advancing sustainable aquaculture practice and provides strategic guidance for the modernization of the industry.