Rhizosphere growth promoting microbes can effectively suppress soil-borne diseases by regulating soil microbial community composition and function. Pepper phytophthora blight caused by Phytophthora capsici is one of the detrimental soil-borne diseases of peppers. However, few studies have been conducted to explore the effects of composite microbial agent inoculation on pepper phytophthora blight suppression and soil bacterial community characteristics. The current study aimed to screen composite microbial agents from healthy soil cultivated with long-term application of organic fertilizers, and to assess their effects on suppressing the occurrence and growth of Phytophthora capsici by plate confrontation and pot experiments, with the latter assessing the efficiency of suppressive pepper phytophthora blight and its linkage with bacterial community characteristics. According to the plate confrontation experiment, the composite microbial agents had higher antagonistic effects on Phytophthora capsica growth. According to the pot experiment, the incidence of pepper phytophthora blight was significantly decreased by 14.3%, and the death rate of pepper was significantly decreased by 23.8% under the treatment of composite microbial agent inoculation compared to the control (inoculation with Phytophthora capsici). The α diversity of bacterial community was significantly decreased, the bacterial community composition was significantly altered and the two-component system function of bacterial community was significantly increased under the treatment of composite microbial agent inoculation. The abundance of Bordetella was negatively correlated with the number of Phytophthora capsici. The results provide a technical support for efficiently suppressing pepper phytophthora blight using composite microbial agents in pepper production.