An accurate evaluation of the dynamic responses on critical components of orthotropic bridge decks is of significance for identifying structural damage and predicting the fatigue life of long-span cable-stayed bridges. However, the traditional finite element (FE) methods are computationally cost-prohibitive for this application. In response, a new multiscale time-varying analysis method based on the dynamic balance equations and FE strategies is proposed and derived theoretically in this paper. Unlike most existing methods, the dynamic responses of this refined model is easily solved through repeated iterations, using the dynamic responses of a large-scale model as the boundary conditions. To validate the effectiveness of the method, a simply supported steel plate beam was used in a field test that demonstrated good correlation between the analytical dynamic responses and the experimental ones. To further validate this method, a case study involving a whole segment model of the Pingtan Bridge orthotropic bridge deck was established and the complex junction area between the plate and longitudinal ribs was modeled using two refinement processes. For comparison, a sufficiently refined model was also developed using ANSYS software based on the traditional FE methods. This study attempted to provide a new high-efficiency analysis framework for accurate analysis of local vibration problems. Under relatively small and easily manageable calculation conditions at each cross-scale processing level, the proposed method meets not only the requirements of global design for actual engineering applications, but also supports further in depth analysis.