In this paper, related with indoor built environment and human comfort, it is applied a numerical software in buildings with complex design. The methodology applies a numerical model which incorporates the building thermal behavior with the human thermal-physiology. The building model uses an energy and mass balance integral equations system solved by Runge–Kutta–Felberg method with error control. In this numerical study, it is analyzed a university building with complex design, in transient conditions and for the winter season. The thermal comfort, using the PMV index, and the air quality, using the carbon dioxide concentration, are evaluated. The building, with 319 compartments and with four floors, is equipped with Heating, Ventilating Air Conditioning system controlled through the PMV index. The results demonstrated that the indoor thermal conditions inside the building are non-uniform and it is important to use specified and adapted control system to guarantee acceptable thermal conditions.