In the field plot experiment,four treatments, including CK (no fertilization+no straw), F (conventional fertilization), SF (straw incorporation+conventional fertilization) and SFR (straw incorporation+conventional fertilization reduced by 15%) were set up to study the effects of rice straw incorporation on nitrogen, phosphorus and chemical oxygen demand (COD) loss through runoff in rapeseed season under rice-rape rotation mode in Chaohu Lake region. The results showed that straw incorporation treatment significantly increased the number of soil microbial bacteria, fungi and actinomycetes, significantly reduced the total nitrogen concentration in runoff, but increased the total phosphorus and COD contents. The number of soil microorganisms was positively correlated with the content of nitrogen, phosphorus and COD in runoff. Compared with F treatment, total nitrogen loss decreased by 16.9%~19.8% and 27.1%~29.3%, total phosphorus loss decreased by 2.4%~4.0% and 4.0%~5.6%in the SF treatment and SFR treatment, while the COD loss increased by 6.1%~10.0% and 2.8%~6.1%, respectively.The results provided a reference for revealing the mechanism of soil microbial biomass and the loss of nitrogen, phosphorus and COD in runoff, and provided a theoretical basis for the rational use of straw incorporation technology.