Bolted joints are widely used in various structures as fastening method because of the convenience in assembly-disassembly. However, loosening of the bolt may cause failure of the structure by reduction of the clamping load. Therefore, it is important to monitor the clamping load of the bolt. According to some previous studies, it has been clarified that the reduction of the clamping load of the bolt decreases the natural frequency of the structure with the bolted joints. This main cause is reduction of the contact stiffness in the jointed part that depends on the contact pressure and the surface topography of the jointed part. In this study, an identification technique using inverse analysis for clamping load from natural frequency of structure with bolted joints has been developed. This technique preliminarily estimates the parameters of the surface topography of the jointed part by using the natural frequency obtained from the known clamping load. And then, the unknown clamping load is estimated by the natural frequency and the parameters estimated preliminarily. In order to verify the effectiveness of the proposed technique, numerical simulations were carried out by using finite element models of the structure with the hollow cylindrical bolt.