Most research in the field of indoor thermal environment control has been devoted to the search for an appropriate on/off temperature of air-conditioning while relatively ignoring the energy-saving effect of the transition period length after air-conditioning turned off. We proposed a control model for the alternate operation between natural ventilation and air-conditioning to measure the delay time of natural ventilation after air-conditioning turned off. We compared the energy consumption of two cooling modes (continuous cooling and alternative operation between natural ventilation and air-conditioning) in different thermal capacity buildings in China’s hot summer and warm winter areas. Furthermore, we obtain the delay time of natural ventilation under different thermal capacity buildings. The results indicate that buildings with more thermal capacity have a greater delay time of natural ventilation. Alternative operation strategy can save at least 15% energy consumption compared with continuous air-conditioning cooling. The results are helpful to guide residents to adjust their use habits of air-conditioning according to the delay time of natural ventilation and to alleviate the pressure of air conditioning energy consumption in hot summer and warm winter areas in China.