A field experiment was conducted to investigate the effects of different doses organic fertilizers from chicken manure on the heavy metals accumulation and availability in soil-plant system, as well as soil microbial community structure in a facility vegetable soil. In addition, the correlation between soil microbial community structure and soil heavy metals was further discussed. The results showed that addition of organic fertilizers from chicken manure increased the shoot fresh weight of the Chinese cabbage. The treatment received 60 t/hm² organic fertilizers was the most significant, where the shoot fresh weight increased by 59.92% compared with control. The application of organic fertilizers increased the shoot Cd, Cr, Cu, Zn and As concentrations of the tested cultivars except of Pb. The contents of soil heavy metals Cd, Cr, Cu, Zn, and As increased with the increase of the amount of organic fertilizers, and all reached the maximum values with the highest increases of 21.30%, 21.58%, 17.40%, 19.40% and 17.43%, respectively. Apparent accumulation of these heavy metals was found in the soil applied organic fertilizer. And the application of organic fertilizers increased the concentrations of soil available Cd, Cr, Cu, Zn, and As. While the total and available Pb concentrations in soil had no significant changes in different treatments. There were significant correlations between the total and available concentrations of soil heavy metals except of Pb, in which the relativity of Zn was the strongest. The results of Phospholipid Fatty Acid (PLFA) analysis showed that the higher PLFA contents were 16:0, 18:1ω7c, 10Me16:0 and 18:1ω9c, and the order of total PLFA and soil microorganism groups PLFA contents showed as M0.5 > M1 > M2 > M4. The results of correlation analysis showed that the total contents of Cu, As and the available contents of Cd, Cr, Cu, Zn, and As were negatively correlated with the total and various groups PLFA contents, and among them, the effects of soil available Cr and Cu on microbial community structure were very significant.