The amount of chemical fertilizer for vegetables is on the high level in China. The use of organic fertilizers to meet the nutrient requirement of crops will be an inevitable practice in sustainable agriculture. In this study, we compared the effects of pig manure fertilizer, rabbit manure fertilizer and chemical fertilizer on yield, quality ofBrassica rapavar.Chinensis, soil physico-chemical properties and microbial community by using two consecutive seasons of three fertilizers in a pot experiment. The results were as follows: (1) In the first season, the fresh yield ofBrassica rapavar.Chinensisapplying chemical fertilizer was significantly (p≤ 5%) higher than those of applying the pig manure and rabbit manure fertilizer, and the results were the opposite in the second season. The total soluble sugar concentration of freshBrassica rapavar.Chinensisapplying rabbit manure fertilizer was significantly (p≤ 5%) higher than those of applying pig manure fertilizer and chemical fertilizer in the first season, and the NO3-N content of freshBrassica rapavar.Chinensison the contrary. (2) The organic fertilizer increased the concentration of total nitrogen, total phosphorus and organic carbon in soil in both two seasons. Rabbit manure fertilizer increased the soil pH and EC and significantly (p≤ 5%) reduced the soil NO3-N content. (3) The pig manure and rabbit manure fertilizer significantly (p≤ 5%) increased the diversity and abundance of soil bacterial ofBrassica rapavar.Chinensis, but had no significant effect on soil fungi. Pearson correlation analysis showed that soil TN, TP, organic carbon content and EC were significantly correlated with soil bacterial α - diversity. There were significant differences (p≤ 5%) in the bacterial community structures between three treatments in two seasons, and significant differences (p≤ 5%) in the fungal community structures between fertilizer treatments while not between two seasons. Pig manure and rabbit manure fertilizer decreased the relative abundance of soilAcidobacteriaandCrenarchaeota, rabbit manure fertilizer significantly increased the abundance ofActinobacteriain the second season. Distance-based redundancy analysis (dbRDA) showed that soil EC, TN, and organic carbon content were key physico-chemical factors in determining bacterial community structure inBrassica rapavar.Chinensissoil, and soil NO3-N, EC, SOC concentration and soil pH in the fungal community structure.