As for the recent need for maintenance of aging structures and tall buildings, the traditional structural inspection and management methods are expected to be enhanced with the automated structural health monitoring system. The system identification technique is deem to be a core deem of the structural health monitoring. In this study, a methodology of structural stiffness estimation is proposed to identify the state space model of the target structure from the dynamic behavior measurement data of the structure. Experimental verification of the physical quantity estimation technique is conducted.