By artificially added micro-ecological agents of Bacillus subtilis, the relationship between microbe quantity and environmental factors was investigated in marine fish pond, to discuss the ecological effects of Bacillus subtilis on marine fish pond. The results showed that the Bacillus subtilis amounts 0.35~1.45×103 cfu/mL in the experiment group, 0.04~0.08×103 cfu/mL in the control group and the phytoplankton biomass (0.1026~0.7632 mg/L in the experiment group and 0.0936~1.5209 mg/L in the control group) were both significantly higher in the experiment group than those in the control group. In the experiment group, the Bacillus subtilis amounts were significantly positive correlative with the diatom abundance (the coefficient = 0.844, P<0.05), but those were significantly negative correlative with the nitrite nitrogen concentration (correlation coefficient = -0.915, p<0.05), if the dissolved oxygen concentration was more than 6 mg/L. In addition, if the dissolved oxygen concentration was too low (< 2 mg/L), Bacillus subtilis had no degradation of the ammonia nitrogen and the nitrite nitrogen in the seawater, but Bacillus subtilis had a significant degradation effects on the ammonia nitrogen and the nitrite nitrogen,  when the dissolved oxygen concentration reached 6 mg/L or more. Thus it can be inferred that the appropriate concentration of Bacillus subtilis can effectively improve the condition of aquaculture water, and further purify the water quality.