Abstract: This paper summarized the effect of organic amendments and chemical fertilizer on soil microbial activity, biomass, and community structure, as well as different microbial feedback to fertilizer inputs because of dissimilar original soil fertility, long/short term fertilizer inputs and amount of fertilizer. Fertilizer inputs is the most important agricultural management practice affecting soil carbon and nitrogen content. Moreover, soil carbon and nitrogen provide a direct source for soil organisms. Furthermore, microbial activity is a live driving force for soil nutrition transformation. Mineral fertilizers have limited direct effects on soil microbial activity, quantity and diversity, but their application can enhance soil microbial activity via increases in crop production, crop residue returns and soil organic matter. Another important indirect effect especially of N fertilization is soil acidification, with considerable negative effects on soil microorganism. Organic amendments provide a direct source of C for soil microorganisms as well as an indirect C source via increased crop growth and crop residue returns. In a word, long term fertilization not only change microbial nutrition transformation way, accordingly affecting soil nitrogen providing capacity and carbon store capacity, but also affect soil sustainability and soil quality.