Abstract:[Background] The highly intensification of shrimp culture industry is facing an increasingly serious problem in water pollution. Simultaneously and high-efficiently degradation of organic matter, ammonia and nitrite in shrimp wastewater is one of important guarantees for the sustainable and healthy development of aquaculture. [Objective] In order to promote sustainable development of Litopenaeus vannamei culture in China, high-efficiently degradation of organic matter, ammonia and nitrite of aquaculture wastewater was developed by combination of immobilized nitrifying bacterial consortia (NBC) and selected Bacillus population. [Methods] High-throughput analysis of 16S rRNA gene was applied to study NBC’s community, which was enriched from the bottom mud of local shrimp ponds. We screened the strain with the highest COD (chemical oxygen demand) degrading capability from five Bacillus strains, and selected nontoxic immobilizing materials with good absorption capacity and ball performance. Further, the immobilized formula was optimized by orthogonal test to improve the mechanical strength. The optimum use concentrations of NBC and selected Bacillus strain were evaluated for high-efficiently degradation of COD, ammonia and nitrite in shrimp wastewater, respectively. [Results] High-throughput analysis of 16S rRNA gene showed that NBC was dominated by Proteobacteria (61.10%), and the abundance of autotrophic nitrifying bacteria in NBC was 12.69% with high diversity. NBC also contained denitrifying or potential denitrifying bacteria with an abundance of 47.44% and photosynthetic bacteria with an abundance of 12.85%. It is an important complement for nitrification under high organic loading and nitrogen removal through denitrification. Bacillus amyloliquefacien YL-10 has the highest COD degradation rate 100% in 48 h. The optimal formula for immobilization is 5% of shell powder, 3% of sodium alginate and 4% of calcium chloride. The mechanical strength of the embedding pellets is 129.68 mN. The immobilization significantly increased the degradation rate of ammonia and nitrite by 128.13% and 130.11%, respectively, but had no obvious effect on COD degradation. The optimum concentration of NBC and YL-10 was 1×108 CFU/mL. Under the joint action of immobilized NBC and YL-10, the concentrations of ammonia, nitrite and COD in shrimp farming wastewater were significantly reduced from (6.32±0.12), (5.69±0.11) and (65.29±1.14) mg/L to (0.03±0.03), (0.06±0.01) and 0 mg/L in 48 h (P<0.05), respectively. The degradation rates were 99.57%, 99.03% and 100%, respectively. [Conclusion] Organic matter, ammonia and nitrite in shrimp wastewater were biodegraded simultaneously and efficiently by combination of immobilized NBC and selected Bacillus population, which provides the scientific data reference for the large-scale practical application in high-density culture of L. vannamei.