Changes in chemical structure have profound effects on the physical properties of epoxy-based materials, and eventually affect the durability of the entire system. Microscopic structural voids generally existing in the epoxy cross-linked networks have a detrimental influence on the epoxy mechanical properties, but the relation remains elusive, which is hindered by the complex structure of epoxy-based materials. In this paper, we investigate the effect of structural voids on the epoxy-based materials by using our developed mesoscale model equipped with the concept of multiscale modeling, and SU-8 photoresist is used as a representative of epoxy-based materials. Developed from the results of full atomistic simulations, the mesoscopic model is validated against experimental measurements, which is suitable to describe the elastic deformation of epoxy-based materials over several orders of magnitude in time- and length scales. After that, a certain quantity of the structure voids is incorporated in the mesoscale model. It is found that the existence of structural voids reduces the tensile stiffness of the mesoscale epoxy network, when compared with the case without any voids in the model. In addition, it is noticed that a certain number of the structural voids have an insignificant effect on the epoxy elastic properties, and the mesoscale model containing structural voids is close to those found in real systems.