The vast majority of geological disasters in loess-covered areas are caused by seepage erosion in loess. Therefore, this paper focuses on the microscopic mechanism of loess seepage erosion, and constructs a loess microstructure model based on particle "core+coat". On this basis, the SEM photos are imported into COMSOL to simulate the micro-scale seepage in the pore domain. Through the actual permeability test, combined with the micro-quantitative information obtained by IPP(Image-pro-plus) and Arcgis, the micro-factors affecting loess permeability are quantitatively analyzed by grey relational analysis. The results show that the dry density affects the porosity of loess and ultimately determines the permeability of loess. Different pore types and proportions lead to different seepage erosion of loess. The erosion process mainly occurs at the junction of pores. The sudden increase of velocity, pressure drop and maximum shear rate at the throat indicate that this area is the main action area of loess seepage erosion. The research results of this paper provide an important theoretical basis for the research and prevention of geological disasters and engineering diseases related to seepage deformation and failure in loess area.