Aims Conventional management (CM), substantial fertilization (furrow and hole application) and flooding irrigation, has led to soil acidification, the decrease of soil bacterial diversity in bamboo forests. Integration of water and fertilizer management (IWF) can effectively improve the utilization efficiency of water and fertilizer, but its effect on soil environment, especially on microbial communit, is still unclear. Methods Here, we used next-generation high-throughput sequencing to compare soil properties and bacterial communities through different fertilization and irrigation methods under IWF and CM. Results Compared to the control group, CM significantly reduced soil pH and bacterial diversity, while IWF increased soil pH, improved soil nutrition status, and increased soil bacterial diversity to a level similar to the control group. Compared with CM, IWF also improved the relative abundance of beneficial bacteria and copiotrophic bacteria community in the soil, and the bacterial community in IWF clustered well with the control group. The structure of the bacterial community was also significantly correlated with soil total nitrogen, hydrolyzable nitrogen, available potassium and soil organic matter, while soil bacterial diversity was mainly associated with soil hydrolyzable nitrogen. Conclusions IWF can play an important role in preventing soil acidification, the loss of soil bacterial diversity, and improving the structure of the bacterial community.