We performed the numerical analysis on the airflow characteristics in the two type of cleanroom systems, which are the axial fan type (AFT) and the fan filter unit (FFU). A computational fluid dynamic model was applied to investigate and compare the nonuniformity, the deflection angle and the air ventilation effectiveness of the two designs of cleanrooms when dampers are adjusted and not adjusted. And the flow-resistance models of the various components were used in this simulation. We know that the airflow characteristics of the cleanrooms are largely affected by damper adjusting And we also find out that the FFU system is superior to the AFT system through the comparison of the cleanroom performance indices.