Two kinds of geotextiles were used to do the Gradient Ratio(GR)tests of a clay-geotextile system, and the Scanning Electron Microscope(SEM)technique was adopted in this study to observe the microstructure of clay after K tests. The objective of this study focuses on the clay filtering mechanism of geotextile from the microscopic point of view. Research results show that: (1)During the clay filtering process of geotextile, the gradient ratio rises rapidly at the initial stage, while after reaching the peak, the gradient ratio drops and tends to be stable with the gradual improvement of the permeability of geotextile-soil system; (2)Some fine clay particles close to the geotextile pass through and escape from the textile during the filtration, which should be the intrinsic mechanism of the permeability improvement of geotextile-soil system; (3)The filtered clay is mainly in the form of poly grain texture with loose structure and larger pores in the clay appear near the geotextile; (4)Geotextiles with different pore sizes and technologies have the same mechanism of clay filtering, while the extents of clogging are different.