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Undesired thermal residual stresses and strains always exist in GaN epitaxial film after the process of metal organic chemical vapor deposition (MOCVD) due to difference in thermal expansion coefficients between the silicon substrate and epitaxial layer. These stresses would mostly result in defects such as dislocations, surface roughness, and even cracks in epitaxial layer preventing further device applications. Effects of the trenches, SiO2 masks and micro patterns made on the silicon substrate on the residual thermal stresses level of the GaN epitaxial layer were studied by simulation with finite element method (FEM). It is found that the thermal residual stresses could be decreased by etching trenches, depositing SiO2 masks and making micro patterns on silicon substrate. These studies can be used to optimize the design and processing of epitaxial growth of high quality GaN epitaxial film on the silicon substrate.