When colloidal particles are deposited in a heat transfer channel, they increase the flow resistance in the channel, resulting in a substantial decrease in heat transfer efficiency. It is critical to have a comprehensive understanding of particle properties in heat transfer channels for practical engineering applications. This study employed the Reynolds stress model (RSM) and the discrete particle model (DPM) to simulate particle deposition in a 3D corrugated rough-walled channel. The turbulent diffusion of particles was modeled with the discrete random walk model (DRW). A user-defined function (UDF) was created for particle–wall contact, and an improved particle bounce deposition model was implemented. The research focused on investigating secondary flow near the corrugated wall, Q-value standards, turbulent kinetic energy distribution, and particle deposition through validation of velocity in the tube and particle deposition modeling. The study analyzed the impact of airflow velocity, particle size, corrugation height, and corrugation period on particle deposition efficiency. The findings suggest that the use of corrugated walls can significantly improve the efficiency of deposition for particles less than 20 μm in size. Specifically, particles with a diameter of 3 μm showed five times higher efficacy of deposition with a corrugation height of 24 mm compared to a smooth surface.