Bolted joints are widely used to assemble various structures, and the conditions of bolted joints significantly affect the dynamic characteristics of structures. This problem causes the difficulties for designing precision machinery or earthquake countermeasures for structures. The aim of the present research is to clarify the contact surface conditions of structures with bolted joints from the microscopic aspect by tribological theory and to develop an estimation method of global dynamic characteristics of structures. First, the method to estimate the natural frequency and damping ratio of structures with bolted joints from the magnitude of tightening torque is proposed. The estimating process is divided into 4 steps, i.e., estimating, (1) tightening force from the tightening torque, and then step by step, (2) contact pressure, (3) contact stiffness and friction loss and finally, (4) natural frequencies and damping ratios of structures. The proposed method was actually applied to the plate and flange structures, and the natural frequencies and damping ratios were first estimated and then those were measured experimentally. It was shown that the calculated results are in good agreement with the experimental results, resulting in the verification of the usefulness and universality of proposed estimation method.