During the in-service use of porous asphalt pavement, debris can clog internal voids, impacting both its long-term performance and maintenance costs. Thus, understanding the clogging mechanism is crucial. This study introduces a novel approach to simulate clogging behavior by coupling the discrete element method (DEM) and computational fluid dynamics (CFD) to analyze various particulate clogging scenarios. The simulations included the effects of vehicle vibrations, the impact of rainwater seepage and their combination. The simulation results reveal that both vibration and rainwater significantly reduce clogging material mass, improving pavement permeability. Particles sized between 0.15 mm and 1.18 mm were identified as the most likely to cause clogging, with the tendency increasing alongside seepage velocity. This methodology provides a comprehensive framework for analyzing real-world clogging mechanisms and offers valuable insights for designing more durable and sustainable porous asphalt pavements.