Plant growth-promoting rhizobacteria (PGPR) are important due to their biostimulant activity. However, most studies focus on epigenetic mechanisms, leaving the microscopic and molecular aspects of multistrain coordination unexplored. In this study, seven PGPR strains were isolated from mangrove forests. These bacteria exhibited various traits such as phosphate solubilization, indole acetic acid production, and siderophore generation. The combination of Sinorhizobium sp. N2-2 and Pseudomonas putida S5 showed the most prominent PGPR activities. Pot experiments and omic-based analyses revealed that PGPR strains significantly promoted the growth of pakchoi and influenced soil physicochemical properties and sucrose enzyme activity. Metagenomic analysis showed that PGPR strains altered the rhizosphere microbial community, enriching genes related to nitrogen cycling, phosphorus transformation, hormone signal transduction, and carbon utilization. Transcriptomic analysis indicated increased energy metabolism and antistress abilities in the host plant. The results suggest that the “composite PGPR” co-promoted plant growth by driving transformations in rhizosphere nutrient cycling, regulating microbial metabolism, and balancing plant physiology. This study provides insights into the coordination between PGPR strains and highlights their potential for sustainable agriculture development.