There is a constant need to predict the dynamic properties of composite materials already at the design stage. A particularly attractive tool for achieving this goal is mesoscale finite element modeling. This paper presents the mesoscale modeling of the dynamic properties of polymer concrete. The method is based on finite element modeling and substructural identification. Substructural identification is a model updating technique based on frequency response functions. It enables the identification of model dynamic properties considering damping. The presented method is used to model the dynamic properties of a polymer concrete beam. In the first step, the mesoscale finite element model is built and then it is decoupled into substructures: a polymer matrix, aggregates, and an interfacial transition zone (ITZ). Next, the dynamic properties of the polymer matrix substructure are updated, and the model is reassembled. Then, second-stage updating takes place, which consists of determining the parameters of the aggregates and the ITZ. The use of substructural identification made it possible to determine the parameters of substructures that do not exist in an independent, isolated form like the ITZ. Moreover, it allows for determining the amount of damping that ITZ brings to the structure.