Abstract: Responses and feedbacks of soil microorganism to fertilization areis important to the evaluation of fertilization effect and establishment of scientific fertilization management. The paper summarized the research results of author’s team in effect of long-term fertilizations, especially single application of organic fertilizer, on soil microorganisms related to the carbon, nitrogen and phosphorus cycling in fluvo-aquic soil. The microbial mechanisms of soil fertility enhancement were also discussed in the paper. The results indicated that for the fluvo-aquic soil in the North China Plain, long term balanced fertilization, especially long term organic fertilization, increased soil contents of organic carbon and other nutrients, the effect was more obvious on soil phosphorus content. This, furthermore, improved soil microorganism community structure, and enhanced soil microbial biomass carbon content, invertase activity, respiration rate and microbial function diversity (carbon metabolic activity), while significantly decreased metabolic quotient and metabolic heat of soil microorganisms. On the contrary, nutritional deficiency, especially phosphorus deficiency, not only decreased metabolic efficiency, but also induced more heat dissipation and CO₂ emission during metabolism of soil microorganisms, which finally decreased soil quality. Long-term application of nitrogen fertilizer enforced soil nitrification activity, and increased amount and diversity of ammonia oxidizing bacteria. Inorganic nitrogen fertilizer was more effective than organic nitrogen fertilizer. In phosphorus-deficient fluvo-aquic soil, rational phosphorus fertilization was essential precondition of scientific application of nitrogen fertilization to promote crop growth and soil fertility, reduce nitrogen loss. Long-term application of phosphorus fertilizer, and balanced fertilization lowered the dependence of crop growth on arbuscular mycorrhizal fungi (AMF), decreased soil AMF diversity and induced differentiation of AMF, which benefited the sustainability of phosphorus-deficient fluvo-aquic soil. An indigenous microorganism of fluvo-aquic soil, Bacillus asahii with unique physiological characteristics and abundant metabolic diversity significantly responded to long-term organic fertilization, and could develop to the dominant species during two to four years. B. asahii could accelerated other microorganisms in the process of organic matter accumulation and phosphorus recycle in fluvo-aquic soil, played a leading role on crop growth and soil fertility increase. The result was favored for understanding the microbial mechanism of effect of long-term organic fertilization on soil fertility improvement in the North China Plain, and for adjusting soil microorganism to serve farmland ecosystem.