The particle motion in a room is affected by the thermal environment and the air supply conditions caused by seasonal changes. In the study, a Lagrangian discrete trajectory model combined with the Eulerian fluid method was adopted to simulate the characteristics of indoor airflow and the diffusion of two typical indoor particles with considering different air supply conditions in different seasons. Specifically, the thermal comfort perception, draught rating (DR) of the indoor personnel, and the contaminant removal effectiveness (CRE, ε) of indoor particles under the influences of displacement ventilation (DV) and underfloor air distribution (UFAD) systems were investigated. The results revealed that when considering the indoor thermal comfort under summer and winter air supply conditions, UFAD was found be more effective than the DV system in protecting the temperature difference of indoor personnel. Additionally, the removal effect of PM1 in the breathing area was superior compared to that of the DV system. Regarding the removal effectiveness of PM2.5, the removal performance of both ventilation systems decreased, but the removal effect of the DV system on PM2.5 in the breathing area (with the largest εl of 1.55) was significantly better than that of the UFAD system under winter operating conditions. It is essential for the selection of the ventilation system to consider the thermal comfort of indoor occupants, as different ventilation systems have varying capabilities to remove particles of different sizes. Therefore, choosing an appropriate ventilation system is crucial for enhancing indoor air quality, and the findings of this study provide a basis for improving indoor air quality.