Pesticide pollution in Sihe watershed, China can have a negatively effect on Nansihu lake and aquatic environment of South-North Water Diversion Project. To understand the process of herbicides transport and best management practices in the watershed, transport simulation of herbicide including atrazine and its transformed products in Sihe watershed performed by SWAT model and field investigation. The results demonstrated that there was a high correlation between the output of herbicides and runoff. The time of herbicides output was mainly concentrated in July and August, which accounted for more than 69% of output in the whole year. The spatial distribution of herbicides load in the watershed was affected by the length of the river and distribution of agricultural land. The output of atrazine distributed primarily in eastern and central region of upstream areas, and catchment outlet of herbicide output was in the middle. However, the spatial distribution of the output of atrazine transformed products including DEA and DIA were similar to their parent compound, which mainly located in the catchment outlet of the downstream areas and the central region in Sihe watershed. The study can provide theoretical support for the management of herbicide migration in the basin.