The invention discloses a system and a method for separating and treating the pollutant sources of a large-scale pig farm. The system comprises a pollutant source separation hog house, an excrement conveying device, an excrement fermenting device, a liquid conveying device, a fecaluria liquid fermenting device, a fence washing water SBR reactor and an ecological wetland, wherein the pollutant source separation hog house adopts the structure that short beams running through the whole hog house in the length direction are established in a hogcote, transverse beams and longitudinal beams are established between the short beams, a slatted floor is paved on the transverse beams and the longitudinal beams, every two short beams and a V-shaped bottom surface form a U-shaped excrement groove, the higher ends of the U-shaped excrement grooves are connected to an excrement collection pool, the lower ends of the U-shaped excrement grooves are connected to a liquid collection pool, and an excrement scrapping system is arranged in each U-shaped excrement groove. The separation of fecaluria from rainwater, drinking residual water and fence washing water and the separation of excrement from fecaluria liquid in advance are realized, so that the problem of difficult solid-liquid separation in subsequent procedures is solved, and the resource utilization and pollution treatment effect is good.