In order to elucidate the advantage of bio-organic fertilizer to vegetable production, a pot experiment was carried out. The effects of two kinds bio-organic fertilizers on rape physiological metabolism, yield, and soil biological characteristics and nutrient content were studied through replacement of 10% to 30% chemical fertilizer with the same amount of the bio-organic fertilizers. Results showed that the bio-organic fertilizer, which was equivalent with the reduced chemical fertilizer, could promote rape growth, chlorophyll content and root activity. Meanwhile, the enhanced activities of antioxidant enzymes (SOD, POD, CAT) and reduced content of reactive oxygen species (MDA, O2? ?) indicated the increased photosynthetic performance and oxidation resistance. Compared with the conventional fertilization (100% chemical fertilizer), the rape yield increased by 4.60% to 24.55% in bio-organic fertilization. The population of soil bacteria and actinomycetes was significantly increased by 111.26% to 210.76% and 12.49% to 34.09%, respectively, but the number of fungi was decreased by 20.37% to 39.68%. With the partial absence of chemical fertilizer, the soil phosphatase, invertase and catalase activities were increased, but soil urease and dehydrogenase activities were decreased, resulting in the increased soil available nutrient and organic matter. The above results suggest that, application of bio-organic fertilizer with the partial absence chemical fertilizer can change soil enzyme activities and available nutrients by improving the number and structure of soil microbial community, and consequently, optimize the rhizosphere environment and increase the root activity and plant stress resistance and photosynthetic ability, finally, enrich soil and increase crop production.