Open graded friction course (OGFC), as a highly permeable mixture, has the characteristics of good friction and splash-and-spray reduction during rainstorms. The limitations of the use of such mixtures include the fact that they are affected by poor durability, including strength and permeability durability issues. In a previous study, oil shale waste, as a fine aggregate in the mixture (with a particle size less than 4.75 mm), could effectively improve the overall properties of OGFC, but the permeability durability was not clear. Thus, a comprehensive investigation of the permeability durability of oil shale waste as a fine aggregate is essential to achieving a better understanding in order to promote its engineering application. In this paper, the long-term permeability when using oil shale waste as a fine aggregate in OGFC was systematically investigated based on a self-developed laboratory physical clogging procedure. The test results illustrated the effectiveness of the utilization of oil shale waste as a fine aggregate in terms of permeability durability. A comprehensive index of the clogging coefficient containing mass, porosity and permeability coefficient was proposed based on gray relation entropy theory, the physical clogging model of COF-OGFC (OGFC containing oil shale waste filler) was established and the clogging speed of COF-OGFC was quantified based on the Mistcherlich growth model. The analysis showed that there is an essential difference in the clogging behavior of permeable pavement in the spring and summer. The maximum clogging degree of the permeable pavement in summer is about 40% higher than that in spring, while the clogging rate is much lower than in the spring, at only about 14%, which indicates that the clogging behavior of permeable asphalt pavement in spring is mostly in the rapid clogging mode, and that in summer is mostly in a slow deposition clogging mode. Moreover, the test results showed that the most important influences on the spring clogging behavior of COF-OGFC were the sandy clogging materials and particle sizes ranging from 150 μm to 1180 μm, which can be used to provide a reference for the design of anti-slip sand.