The improvement of saline-alkali land plays a key role in ensuring food security and promoting agricultural development. Saline soils modifies the response of the soil microbial community, but research is still limited. The effects of applying phosphogypsum with rice cultivation (PRC) on soil physicochemical properties and bacterial community in soda saline-alkali paddy fields in Songnen Plain, China were studied. The results showed that the PRC significantly improved the physicochemical properties of soil, significantly reduced the salinity, increased the utilization efficiency of carbon, nitrogen, and phosphorus, and significantly increased the activities of urease and phosphatase. The activities of urease and phosphatase were significantly correlated with the contents of total organic carbon and total carbon. A redundancy analysis showed that pH, AP, ESP, HCO3−, and Na+ were dominant factors in determining the bacterial community structure. The results showed that PRC could improve soil quality and enhance the ecosystem functionality of soda saline-alkali paddy fields by increasing nutrient content, stimulating soil enzyme activity, and regulating bacterial community improvement. After many years of PRC, the soda-alkali soil paddy field still develops continuously and healthily, which will provide a new idea for sustainable land use management and agricultural development.