The subgridding boundary condition (SGBC) based modeling of thin composite layer in Finite-Difference Time-Domain (FDTD) simulation of enclosures breaks the constraint that the mesh size should be less than the smallest dimension of thin composite layer to get more accurate results, and therefore greatly reduce the computational cost. A large-scale parallelization platform JASMIN based modeling method of SGBC-FDTD was developed. The thin composite layer can be automatically modeled and adaptively allocated in the developed parallelized SGBC-FDTD code. The parallelized SGBC-FDTD algorithm was used to analyze the electromagnetic shielding effectiveness of enclosures containing composite thin layers with different electromagnetic properties in the frequency range of 0.1-1.0 GHz. The results show that shielding effectiveness predicted using the parallelized SGBC-FDTD algorithm are in good agreement with the ones calculated by a full-wave analysis software, while the calculation efficiency is significantly improved.