A strain of Bacillus pumilus BP-171 with the ability of heterotrophic nitrification-aerobic denitrification was isolated from a shrimp culture pond and showed good denitrification ability under laboratory conditions. In order to investigate the effects of strain BP-171 and its combinations with different carbon sources, i.e., poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) and molasses, on the growth performance of shrimp, water quality and bacterial community in culture system of Penaeus vannamei, this experiment was set up. Four experimental groups were designed, i.e., group B applied with a single B. pumilus BP-171, the BP added with BP-171 and PHBV, the BM added with BP-171 and molasses, and the control DZ without the probiotic and carbon source. The results showed that the specific growth rate, final body weight, gross weight, feed efficiency rate and survival rate of shrimp in the BP and BM groups were better than those in the control (p < 0.05), while the survival rate and gross weight of shrimp in group B were also better than those in the control (p < 0.05). Among them, the best growth performance of shrimp was observed in the group BP. The concentrations of ammonia, nitrite, nitrate and total nitrogen were significantly lower in all treatment groups than in the control (p < 0.05). The lowest concentrations of ammonia and nitrite were found in group B, while those of nitrate and total nitrogen were found in group BP (p < 0.05). The concentrations of dissolved organic carbon and total organic carbon in both BP and BM groups were significantly higher than in group B and the control (p < 0.05). Compared to the control, the abundance and diversity of the bacterial community in water did not change with the addition of probiotics and carbon sources. However, altered structure and predicted function, as well as improved stability of the ecological network of the bacterial community, were observed in water. In view of the above, the addition of B. pumilus BP-171 and PHBV significantly promoted the growth performance of shrimp, effectively improved water quality, and enhanced the stability of the ecological network of bacterial communities in water, which could have great potential for the application in intensive culture of P. vannamei.