Changes in rhizodeposits of crops under elevated CO2 (eCO2) and elevated temperature (eT) may substantially impact on soil microbial community, which in turn affects soil carbon and nutrient cycling. However, the responses of soil bacterial community to long-term eCO2 and eT are not fully understood. A seven-year field experiment using open-top chambers was carried out with soybean (Glycine max L. Merr.) and maize (Zea mays L.) grown in a Mollisol soil under ambient CO2 (380 ppm), eT (2.1 °C increase in air temperature) and eTeCO2 (elevated temperature plus elevated CO2, 2.1 °C increase in air temperature and 700 ppm CO2). Soil DNA was extracted for Illumina MiSeq sequencing. The principal coordinate analysis showed that changes of bacterial community structure due to eT and eTeCO2 were greater in soybean- than maize-grown soils. The eT increased the relative abundances of Gaiella and Bacillus in Actinobacteria and Firmicutes, but decreased those of Nocardioides and H16 in Actinobacteria and Proteobacteria, respectively. The magnitudes of responses of seven genera sensitive to eT varied between soybean- and maize-grown soils. The eTeCO2 decreased the relative abundance of Bacillus and increased those of Gaiella, Streptomyces and Mizugakiibacter. The abundances of Gaiella, Gemmatimonas, and Mizugakiibacter under eTeCO2 were higher in soybean- than maize-grown soils. The redundancy analysis showed that soil organic C, moisture, nitrate, microbial biomass N and Olsen-P significantly affected soil bacterial community composition. All these results indicate that long-term eT increased the abundance of bacterial community and shifted their composition compared to the ambient control. In addition, the bacterial community composition under eTeCO2 was more stable in maize- than soybean-grown soils. The study suggests that warming and crop species may interactively affect the stability of bacterial community linking to the sustainability of soil eco-function in future cropping systems.