The recent years have seen a surge in research on the material and structural response of composites using homogenization based hierarchical modeling method. Conventionally, periodic boundary condition (PBC) is applied on the RVE boundary. The micromechanical results are inputted to a homogenized-based constitutive model to give a macro-scale description. However, when the heterogeneous microstructure is under very high strain rate loading conditions, PBC does not represent the accurate effect of stress wave propagation. Thus, it will reduce the accuracy of the calibrated tensor field in the multiscale model. In order to increase the accuracy of the homogenization model, this study introduces a new space-time dependent boundary condition (STBC) for 3D microscopic RVE subjected to high strain rate deformation in explicit FEM simulation. The advantages of the STBC are discussed by comparing with time-dependent averaging results of examples using PBC. The proposed STBC offers significant advantages over conventional PBC in the RVE-based analysis of heterogeneous materials.