Rod-fastened rotor is the core rotating section of the heavy-duty gas turbine. To accurately analyze its dynamic characteristics, the contact model for the disk contact interface needs to be defined and established. Traditional statistical contact models, including the elastic model and elastoplastic model, cannot describe microscopic atomic behavior during the contact process of asperities, while the microscopic contact behavior of the asperities is one of the main factors in affecting the contact stiffness of the rough surface. In this work, the molecular dynamics simulation of the microscopic contact behavior of the rough surface is carried out and the semi-analytical model is built upon that. The semi-analytical model is later combined with the Timoshenko beam element in modeling the rotor system. The influence of plasticity index and surface roughness on the contact model and dynamic characteristics of the rotor is analyzed. Moreover, the experimental tests of natural frequencies and mode shapes are carried out. The results show that the proposed semi-analytical contact model is effective and more accurate compared to other elastic and elastic-plastic contact models.