Abstract: Soil microflora is an important part of soil ecological environment. The stability of soil microflora plays an important role in plant growth. Except for the plant growth promoting ability, some endophytes also significantly impact soil microflora. In this review, quantities of studies are summarized and effects of endophytes on soil microflora and the regulatory mechanisms are also discussed. Endophytes not only improve soil microbial composition and biomass, but also enhance soil enzyme activities and the expression of related enzyme genes. The mechanisms of these effects mediated by endophytes are complex. Living in soil, endophytes occupy the same niches and struggle for the sources of carbon and nitrogen with soil microbes. Meantime, endophytes provide plenty of carbon and nitrogen sources for soil microbes by degrading litters in the soil. They also produce some antimicrobial active substances and organic acids to affect soil microbes. In addition, endophytes regulate soil microorganisms by promoting the release and degradation of complex organic compounds, such as ligin and phenolic allelochemicals. Furthermore, endophytes reduce the toxicity of heavy metal in soil. In addition, the application of endophytes is discussed. The deficiencies in the existing researches are pointed out and the further researches are also put forward.