This paper reports the application of a hybrid ventilation system to a high-rise building, especially on the indoor environment in the building and the effects of the system on the variation of thermal load. The hybrid ventilation system executes natural ventilation while operating air-conditioning systems. The number of the system applications has been increasing, but the change of thermal load by the operation method is not estimated precisely, which leads to less reliability in energy conservation effect. By the hybrid ventilation system, the thermal environment may become worse with the draft caused by natural ventilation. It is especially important to consider indoor thermal environment when ventilation openings are located in occupied zone of the building. In this paper, hybrid ventilation system applied to a super high-rise building in Tokyo, Japan is presented. The evaluation on indoor environment by measurement is discussed, which shows little problem on thermal environment. The effect of thermal mass is important for thermal load estimation, especially when utilizing "night purge" of natural ventilation. The change of thermal load is estimated by the simulation validated by the reproduction of the shift in slab temperature with estimated indoor heat generation and outdoor condition. The annual cooling load reduction is evaluated to be about 21%.