A water-based floor radiant heating system (WFRH) is used in a Solar Decathlon House for temperature and thermal comfort control. To minimize the energy consumption, while maintaining the thermal comfort, computer simulations are utilized to evaluate different control strategies before actual implementation. However, there are two potential challenges which have not been addressed before: first, the availability and credibility of material thermal property data or sensor data could be problematic. Second, the optimum control algorithm comes mainly from a candidate pool based on and limited by operator’s experience. This paper presents the study of system identification and numerical optimization application in the WFRH. The combined approach is to improve the reliability of building simulation in a real system operation. The formulating process of system identification and optimization has been detailed in this paper. The integral method can be generalized to other building control systems.