The improvement of aeration conditions in the rhizosphere is beneficial for crop growth and productivity. However, its effects on the soil microbial community are less known. Due to microbial sentivity to environmental changes, transporting micro-nano bubble water (MNBW) to the crop rhizosphere is expected to shift soil microbial community. A two-year MNBW irrigation field experiment consisting of two mixing ratios of MNBW and groundwater (high level of MNBW, 1:0 and low level of MNBW, 1:4), and a control treatment (CK, groundwater without MNBs), was conducted in a sugarcane plantation station at Guangxi, China. The results indicated that MNBW irrigation, particularly with the high level, changed the composition and potential functionality of the soil bacterial community, reduced its diversity and altered microbial co-occurrence patterns. Structural equation modeling (SEM) demonstrated that MNBW irrigation directly affected soil microbial community and soil fertility, and indirectly promoted sugarcane yield. Overall, this study highlighted that the application of MNBW improved plant yield, and this response was strongly associated with a better nutritional content of MNBW irrigated soils and changes in the bacterial community.