Particulate deposition effects on flow and heat transfer in an internal swirl tube subjected to fly ash ingestion were investigated by constructing an unsteady simulation framework, in which a particle–wall interaction model and a mesh morphing technique were implemented. Swirling flows in the swirl tube were induced by two tangential jet nozzles. Particles having a mean diameter of 6.5 μm were released from the nozzle inlets to model an exposure duration of 4500 h for engine operation in real fly ash environment using scale factors in the unsteady simulations. Particle deposition and its dynamic process were examined, and the effects of deposition on the swirling flow were quantified by comparing time-averaged velocity profiles, vorticity, pressure loss, and heat transfer with those from a clean tube without deposition. Results reveal that the most upstream section of the swirl tube captures the majority of the particles and the deposition distributions show a spiral pattern over the tube wall. The total mass of the deposits within the tube linearly increases, while local deposition thickness has a nonlinear relationship with the exposure time due to the interaction of the particles with the swirling flow. The deposition can generate a maximum of 15% reduction in cross-sectional area of the tube within the exposure duration, resulting in a reduced swirl number, because of the accelerated axial velocity and the decreased circumferential velocity, and further lower heat transfer in the downstream section of the tube relative to the clean tube case. However, as the heat transfer in the upstream deposition section is enhanced by the roughness due to the deposition, area-averaged heat transfer throughout the entire swirl tube is slightly improved by 4.0% but simultaneously a 179% higher pressure loss is observed, leading to an overall thermal performance value of 0.79 (relative to 1.0 for a clean tube), indicating substantial degradation of cooling performance in the fouled swirl tube.