The modeling of the heating, ventilation, and air conditioning (HVAC) system is a prominent topic because of its relationship with energy savings and environmental, economical, and technological issues. The modeling of the HVAC system is concerned with the indoor thermal sensation, which is related to the modeling of building, air handling unit (AHU) equipments, and indoor thermal processes. Until now, many HVAC system modeling approaches are made available, and the techniques have become quite mature. But there are some shortcomings in application and integration methods for the different types of the HVAC model. The application and integration processes will act to accumulate the defective characteristics for both AHU equipments and building models such as nonlinear, pure lag time, high thermal inertia, uncertain disturbance factors, large-scale systems, and constraints. This paper shows types of the HVAC model and the advantages and disadvantages for each application of them, and it finds out that the gray-box type is the best one to represent the indoor thermal comfort. But its application fails at the integration method where its response deviated to unreal behavior.