Porous asphalt pavement is credited with a variety of environmental benefits, including improvement of stormwater management, enhancement of underground water quality, mitigation of heat-island effect, and reduction of traffic noise. However, the sustainability of these functions is a major practical concern as they are seriously affected by clogging in the porous pavement. This study proposed three-dimensional discrete element simulation to evaluate degradation of air voids in the double-layer porous pavement under traffic loading. Double-layer porous asphalt pavement having 25 mm upper layer with 20% porosity and 40 mm lower layer with 22% porosity was designed. Temperature-dependent micromechanical parameters of contact models in asphalt mastic were determined by conducting laboratory dynamic creep test. The virtual wheel tracking test was verified and performed on the virtual double-layer porous asphalt pavement specimen. It has demonstrated that the connected voids content is decreased by 19.8%, 30.2%, and 1.7% in the whole specimen, within the loading and non-loading areas of the specimen, respectively as strain is increased from 0.01 to 0.12 during the wheel tracking test. Furthermore, the long-term degradation model of air voids in the double-layer porous asphalt pavement under traffic loading was formulated. At service life of 20 years, the connected voids content is decreased by 9.9%, 16.2%, and 0.7% in the whole specimen, within the loading and non-loading areas of the specimen under light traffic, respectively. When subjected to medium, heavy, and extra heavy traffic for 20 years, the connected voids content within the loading region of the specimen is reduced by 18.2%, 19.5%, and 20.4%, respectively. The long-term degradation of air voids in the double-layer porous asphalt pavement has important implications on its performance and functionalities. This study develops a methodology to predict air voids degradation of the double-layer porous asphalt pavement under traffic loading, which provides useful information for pavement engineers in the design of porous asphalt pavement.