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The particle penetration factor is an important parameter to determine the concentration of indoor particles. In this paper, a mathematical model for calculating this parameter was established by combining with the decay of the indoor PM2.5 and CO2 concentrations measured in a bedroom with an air cleaner. The convergence of the penetration factors was analyzed under different working conditions. The results show that the particle penetration factors converge to stable values within the range of 0.69 to 0.84 close to the value from the empirical formula when the indoor PM2.5 concentration decays to stable values. When the role of particle deposition is ignored, the penetration factors at the low and middle airflow modes are 0.78 and 0.69, respectively. The particle penetration factors are mainly determined by the clean air delivery rate (CADR) of the air cleaner, clearance airflow, and I/O ratio during the balanced phase when the roles of indoor particle deposition and exfiltration can be ignored. This work can provide a convenient method for the calculation of the particle penetration factor.