The classical approach to thermal comfort control utilizes fully automatic controllers for temperature, humidity, and other variables. Although commonly used, such systems may need much energy. If speed is not the priority, natural airflow may be considered for the control process. However, this would require a model including airflow changes caused by the opening of windows and doors, which has not been found in the literature yet. This article presents a novel multi-layer control system for thermal comfort control that uses an original graph-based representation of opening and closing doors and windows. It allowed us to model airflow dynamics. The system has two essential advantages. Firstly, the natural airflow between adjacent zones may help the automatic controllers achieve their goals and save energy. Secondly, including the windows and doors into the model lets the human play an active role in an eco-aware control process, which corresponds with the “human-in-the-loop” trends. The concept has been illustrated with an example house with four types of thermal comfort zones. The optimization approach based on finding the optimal subgraph of opened windows and doors between chosen zones led up to 5% energy savings of the electric actuators, compared with the classical fully automated structure.