Drought stress in soil can be crucial to plant yield because it reduces growth rate, stem elongation, leaf expansion, and stomatal movements. Several microorganisms in the rhizosphere soil are free-living, soil-borne bacteria that aggressively colonize the rhizosphere or plant roots. The efficiency of rhizosphere microorganisms in promoting plant growth has been demonstrated in numerous greenhouse and field studies on different plant species. However, studies on the influences of continuous drought on rhizosphere microbial populations and community diversity are limited. Therefore, a bacterial strain with known positive effects on plant growth, named YT3, was used in the present study to investigate the effect of continuous drought on soil bacteria population. The bacterial strain was isolated and screened using the serial dilution method on the rhizosphere soil of sweet cherry (Cerasus pseudocerasus) growing fields. YT3-gfp was labeled with green fluorescent protein into plant growth-promoting rhizobacteria YT3. A pot experiment was conducted to determine whether continuous drought stress (continuous drought of 7, 14, 21, 28, 35, and 42 d) could benefit YT3-gfp activities in sweet cherry rhizosphere soil. In addition, the effect of continuous drought stress on microbial populations, as well as the community diversity in rhizosphere soil was investigated by plate culture method and terminal restriction fragment length polymorphism (T-RFLP) analysis. The results showed that the YT3-gfp populations in the rhizosphere soil were 8.75 to 28.77 times higher than those in the non-rhizosphere soil of sweet cherry. The YT3-gfp amount increased simultaneously with the continuous drought stress in rhizosphere soil or non-rhizosphere soil; however, a decrease was also observed during the severe drought stress period. YT3-gfp in the rhizosphere was more easily subjected to drought stress than that in non-rhizosphere soil. The maximum YT3-gfp amounts in rhizosphere soil and non-rhizosphere soil were observed on day 21 at 166 × 10⁴ CFU/g and on day 28 at 6.7 × 10⁴ CFU/g. Along with continuous drought stress, bacteria and actinomycete populations, as well as the total microorganism amounts, first increased then decreased; however, fungus populations in the rhizosphere soil of sweet cherry decreased continuously. Continuous drought stress significantly influenced the T-RFLP profiles in the rhizosphere soils of sweet cherry seedlings. The T-RFLP profiles showed that some special terminal restriction fragments (T-RFs) decreased, and some T-RFs disappeared with continuous drought stress. However, some T-RFs appeared under certain drought stress conditions. The highest Margalef and Shannon indexes and the lowest Simpson's index were observed on days 21 or 28 after continuous drought stress. Moreover, the principal component analysis for T-RFs of the different treatments showed that an independent group of bacterial community structure was formed during continuous drought stress in 14 days to 35 days, indicative of the diversiform community structure. The other two independent groups were formed on days 7 and 42 after continuous drought, respectively, indicative of the simplified community structure. Consequently, soil bacteria community structure was significantly influenced by continuous drought stress. Certain drought stress can improve the bacteria and actinomycete populations, and increase the microbial community diversity. Therefore, certain drought stress is beneficial to the sustainable microbial community structure in sweet cherry rhizosphere soil.