The long-term stability and homogeneity of thoron progeny are key to the performance of a thoron calibration chamber, which is vital to quality assurance in measuring thoron progeny. It is difficult to build a stable and high level of thoron progeny because the half-life of Pb-212 is long. Thus, a stable and efficient compensation system is necessary to compensate for the loss of thoron progeny caused by sampling, decay, and wall deposition. In this paper, a thoron progeny compensation system at the University of South China is optimized, and a suitable ventilation rate regulation method is developed that can effectively improve the activity level and stability of output rate for thoron progeny. The experimental results show that the Pb-212 activity output rate increases by 28% and that the output rate is more stable. Under these conditions, the time for the output rate of ThB activity to reach stability is reduced by 33%, and for ThC, the time to reach stability is reduced by 40%. Furthermore, the concentration ratios of ThC and ThB range from 0 to 0.82.