In order to study the effect of adding Bacillus in the pond on the physicochemical factors and bacterial community structure, high throughput sequencing technology was used to analyze the bacterial community structure in water and sediment of the experimental group (adding Bacillus in pond) and the control group (without adding). At the same time, the physicochemical parameters in water and sediment of the two groups were collected. The results indicated that the contents of TN, ${\rm{NH}}_4^ + $-N, ${\rm NO}_3^-$-N in water were significantly lower than those of the control group (P<0.05), but the contents of ${\rm{NO}}_3^ - $-N, ${\rm{NH}}_4^ + $-N, TN and TP in sediment were significantly higher than those of the control group (P<0.05). The abundance of Chlamydomonas debaryana, Zymomonas, Roseomonas, Dechloromonas and Chitinophaga in water of the experimental group was significantly higher than those in the control group (P<0.05). Among these bacterial communities, Dechloromonas and Chitinophaga have the function of removing ${\rm{NO}}_3^ - $-N, and Zymomonas and Roseomonas have the function of denitrification. The Chao1 and Shannon indexes in water of the experimental group were significantly higher than those in the control group (P<0.05). Hydrogenophaga, Geothermobacter and Haliscomenobacter were negatively correlated with ${\rm{NO}}_3^ - $-N and TP, and positively correlated with ${\rm{NH}}_4^ + $-N and TN. Above all, these results showed that adding Bacillus to the pond would lead to the variations of bacterial community structure, thus realizing the regulation of physicochemical factors in the pond. And the results are useful for reducing the pollution of aquaculture tail water to water environment.