Most applied strategies during the building design process require careful consideration of indoor air quality and thermal conditions. This requires a detailed analysis involving multi and interdisciplinary efforts during the design process and thus, in turn, manifold interactions among various analysis methods and their simulation tools. An undesired consequence of this activity may be major problems in terms of data clashes and data losses. These difficulties may be overcome by utilizing a three-dimensional (3D) building model that not only includes the building's functional and physical specifications but also incorporates its thermal capacity and environmental dynamics. For this, building information modeling (BIM) can be employed as a base. The interoperability of the programs thus utilized need to be identified and ensued, as this is not yet clearly defined in the literature for these complicated analysis methods. This study thus aims to improve the building design process by developing a method to determine the interoperability of the utilized programs for evaluating a building's energy performance and indoor comfort through the BIM approach. A case study is conducted to verify the applicability of the proposed method and to identify the interoperability limits during the data exchange. To this end, three main analysis models are developed and evaluated. The architecture of the building is developed with the 3D building model as specified by the building's physical conditions; the indoor comfort conditions are developed with the computational fluid dynamics (CFD) of natural ventilation as specified by temperature, humidity, and air velocity; and energy performance is developed with a building energy model specified by the building architecture and its systems. These are then all integrated through a BIM platform. Therefore, the complexity of software integration is eliminated by the BIM-based proposed methodology.