Abstract: The effects of different fertilizer treatments on soil ecological characteristics of microorganism of fertilizer omission plots (CK) and whole NPK plots (NPK) in a long-term fertilization experiment for rice were investigated. The results show the soil enzyme activity and microbial biomass C were significantly increased under the fertilization, and organic manure has much larger effect than that of the pure chemical fertilizers (CF). The application of organic manure in the CK soil and the NPK soil has similar effect on enzyme activity and microbial biomass C. The results of PLFAs show the composition of the microbial community of the CK soil is changed by different organic fertilization treatments. Organic manure application has substantial impact on the microbical diversity of the soil. It mainly increased the mole percentage of the PLFA biomarker unsaturated fatty acids, cyclopropane cy19∶0 for bacteria and fungi, and reduced the 10 Me18∶0 mole percentage of the PLFA for actinomycetes.