As the excessive use of chemical fertilizers harms organisms and adversely affects the soil environment, the replacement of chemical fertilizers with biological fertilizers has attracted widespread attention as an environmental protection strategy. In this study, the effects of rhizosphere bacteria inoculation on growth of Pinus sylvestris var. mongolica seedlings, soil parameters, soil microbial community structure, and the biocontrol of damping-off were studied by pot experiments. The results showed that all three rhizosphere bacteria (Pseudomonas chlororaphis, Pseudomonas extremaustralis, and Acinetobacter lwoffii A07) tested exhibited growth-promoting properties, such as the production of indole-3-acetic acid, hydrolase, siderophores, and hydrogen cyanide; nitrogen fixation; and phosphorus solubilization. The application of the three bacteria increased plant biomass, root structure, and nutrient content and also increased soil nutrient content and enzyme activity. Bacterial inoculation promoted the growth of beneficial bacteria and antagonistic bacteria by adjusting the physicochemical properties of the soil, thereby improving the bacterial community structure. Among the soil features, available nitrogen, total nitrogen, available potassium, and urease activity were the main influencing factors. In addition, it was also found that bacterial inoculation significantly increased the activities of plant superoxide dismutase, catalase, peroxidase, and other defense enzymes; enhanced plant disease resistance; effectively inhibited damping-off; and promoted plant growth. In summary, the application of three rhizosphere bacteria systematically affected the interaction between plants, soil parameters, and soil microbial communities. These results provide a basis for understanding how rhizosphere bacteria promote the growth of P. sylvestris var. mongolica, thereby offering a promising sustainable alternative to chemical fertilizers.