In this study, the performance of an axial cyclone separator was analyzed by comparing dust collection efficiency, pressure drop, velocity distribution, and re-entrainment between conditions with and without water in the dust bin. Based on experimental and simulation results, it was found that when the dust bin was filled with water, the cutoff size decreased by 0.2–0.8 µm compared to the dry condition, leading to an improvement in collection efficiency, although a slight increase in pressure drop was observed. When water was present in the dust bin, tangential velocity was lower than in the dry condition, while axial velocity in the direction of gravity increased. This effect contributed to the enhancement of collection efficiency. In re-entrainment experiments, when clean air was supplied after dust was collected in a dry dust bin, the previously accumulated dust was re-entrained. However, when dust and water were mixed and stored in the dust bin, no re-entrainment occurred. These findings confirm that filling the dust bin with water in an axial cyclone separator is an effective method to simultaneously improve collection performance and prevent re-entrainment without requiring structural modifications. The results of this study are expected to have high applicability in various industrial settings.