To elucidate the effects and mechanism of complex microbial agent on the improvement of soil chemical and biological properties and the promotion of plant growth, the effects of different dosages of convention and sterilization complex microbial agents on growth, physiological metabolism of cotton and biological characteristics and nutrient contents in rhizosphere soil were investigated. Results showed that adding complex microbial agent increased chlorophyll content in cotton leaves, enhanced the activities of antioxidant enzymes (SOD, POD, CAT), reduced the contents of reactive oxygen species (MDA, O₂^?-) in both leaves and roots, then increased photosynthetic performance and the ability to resist oxidative stress. Besides, it reduced soil pH, increased the amounts of soil bacteria and actinomycetes, decreased the number of soil fungi, increased the activities of soil urease, phosphatase, invertase and dehydrogenase, increased the contents of available nutrients and organic matter in soil, thus, improved the rhizosphere environment, and promoted cotton biomass accumulation and disease resistance. The above indexes except soil nutrient contents influenced by convention complex microbial agent were better than sterilization complex microbial agent, and the dosage of 10 L/667m² got the more obvious effect. In summary, the application of complex microbial agent could change soil enzyme activities and available nutrients by improving the number and structure of soil microbial community and soil pH, thus optimize the rhizosphere environment and increasing plant stress-resistance and photosynthetic ability, and consequently enrich soil and increase crop production. What’s more, the beneficial live bacteria in complex microbial agent had a particularly important positive effect on plant growth and soil improvement.