To form microbial nanoball, EM active calcium was immobilized on nano-silica carrier consisting of pond sediment, zeolite powder and nanosilica. Through real-time monitoring of pH, dissolved oxygen (DO), chemical oxygen demand (COD) and ammonia nitrogen (NH4+-N) aquaculture wastewater, the purification effects of Microbial nanoSilica Ball on aquaculture wastewater under different mud-water ratio condition were studied. The results showed that the purification effect reached best in 3-6 days for all treatments and was better for mud-water ratio of 1:2.7. In this mud-water ratio, it was indicated that pH was maintained at 7-8.5 which was an optimum value for the aquaculture, the content of DO was increased by 82.16% compared with the initial value and the removal rate of COD and NH4+-N was 57.80% and 54.60% respectively.