Organic farming is an eco-friendly and sustainably agricultural system. Recently, with consciousnesses of environmental protection and food safety, organic farming becomes popular cultivation practice. Organic fertilizers not only provide crops with nutrients, but also become an energy source of soil ecological system. However, different organic fertilizers affect soils differently. The objective of this study was to evaluate the effect of long-term application of different organic fertilizers on soil microbial community structure and chemical properties. Treatments include: cattle dung compost (CDC), hog dung compost (HDC), chicken dung compost (CHC), soybean meal (SBM), pea residue compost (PRC) and rotational application (RA). After cultivation for 13 years and 87 crops, the soils were sampled for analysis. The results showed that application of HDC increased the contents of soil organic matter, total phosphorus (P) and total potassium (K), and this treatment also had the highest rate of basal respiration, nitrification rate, and enzyme activities. On the other hand, application of SBM had the lowest contents of organic matter, enzyme activities, and the other biological indices. More nitrogen (N) in SBM are labile nitrogen compounds, therefore, the residue N in non-labile pool of soil with SBM treatment was significant less than other treatments. The contents of non-labile P in soils with treatments of HDC, CHC, and RA were greater than other treatments. Different organic fertilizers had no effect on soil microbial community structure. However, there was significant difference in actinomycete/bacteria ratio among treatments. Different organic fertilizers also resulted in significant difference in the composition in bacteria and fungi community, respectively. The bacteria community compositions of CHC and HDC treatments were different from other treatments. The results also showed that the fungi community composition of soils of HDC, SBM and PRC treatments were different from the other treatments.