The indicators of soil microbe (the microbial communities and diversity,soil microbial biomass,soil microbial activity),soil enzymatic activity and soil animals are three important biological indicators that token soil quality. These indicators are easily affected by soil environmental factors and actives of men,such as soil water,soil temperature,cultivation and application of organic and inorganic fertilizers. We summarized the effect of organic and inorganic fertilizers application on these bioindicators in soil in this paper.