Agricultural non-point source (NPS) pollution is a growing environmental problem, contributing much to water eutrophication in China as well as in other parts of the world. NPS pollutants are heterogeneously distributed and discharged from agricultural lands and other sources, and extremely hard to control by technical measures. Hence, control of the water quality problems caused by agricultural NPS pollution becomes difficult if recommended best management practices (BMPs) can’t be well implemented. In this paper, current research progress related to distinguishing agricultural NPS pollution sources was reviewed. Three pivotal methods for identifying agricultural NPS pollution sources were introduced and the advantages and disadvantages of each approach were discussed. Finally suggestions were presented on better identifying agricultural NPS pollution sources in China.