[Objective] This study aimed to investigate the effects of different types of microbial agents applied during the jointing stage of wheat in a wheat-maize rotation system on soil properties. [Methods] Field experiments were conducted from 2022 to 2024. Four treatments were set up：a water control（CK），application of auxin-producing microbial agent（BS），application of microbial agent（PM），and application of biocontrol microbial agent（BSA）. The impacts of different agents on soil chemical properties，bacterial community structure，and wheat yield were examined. [Results] In the 0—20 cm soil layer，the application of various microbial agents significantly improved soil chemical properties compared to CK（p<0.05）. The PM treatment had the most significant effect on increasing soil alkali-hydrolyzable nitrogen and available phosphorus content（p<0.05），with increases of 22.60%-29.61% and 21.63%-37.51%，respectively，and a significant decline in pH（p<0.05）. There was no significant difference in available potassium content among treatments. In the 20—40 cm soil layer，available phosphorus content in the PM treatment was significantly（22.05%）higher than that in CK（p<0.05），while there were no significant differences in pH，organic matter，alkali-hydrolyzable nitrogen，and available potassium content among treatments. Compared to CK，the application of all microbial agents significantly increased the α -diversity index of rhizosphere soil bacteria（p<0.05），with an increase of 0.73%-7.43%. The application of microbial agents significantly affected the relative abundance of dominant bacterial phyla in the soil. Ninety days after application（p<0.05）， compared to CK， the relative abundance of Proteobacteria in the BS， PM， and BSA treatments increased significantly by 2.70%， 5.42% and 3.71% （p<0.05）， respectively， while the relative abundance of Gemmatimonadetes in the PM treatment decreased significantly by 4.75%（p<0.05）. The relative abundance of bacteria with biocontrol and growth-promoting functions in the rhizosphere soil of all microbial agent treatments was higher than that in CK，while the relative abundance of the pathogenic Nocardioides，which has disease-inducing effects，was significantly reduced at both 15 and 90 days after application（p<0.05）. Compared to CK，wheat yield in the microbial agent treatments increased significantly by 8.28%-20.43% from 2022 to 2023 and by 5.70%-16.23% from 2023 to 2024（p<0.05），with the PM treatment showing the most significant effect. [Conclusion] The application of microbial agents during the jointing stage of wheat effectively activates soil nutrients，enhances bacterial diversity and the abundance of biocontrol and promotive functional bacteria，and increases wheat yield，with the application of Paenibacillus mucilaginosus PM12 being the most effective.