The aim of this work is, using finite element analysis, to study the effects of thermal load and rotation speed on the structural integrity of a substrate holder module in an MOCVD reactor. Several loading conditions are considered, including thermal load and rotational speeds of 0-1500 rpm. In addition, the wafer bow and residual stress of GaN film grown on silicon or sapphire wafer are systematically studied. Simulation results indicate the variation of critical stress with rotation speed in all of the components is small. Given a similar heat source in the MOCVD reactor, temperature of the upper components such as susceptor, substrate holders, and wafers is higher in the case of sapphire wafer than that in the case of silicon wafer. The temperature gradient of upper components is greater for the silicon wafer case. A greater temperature gradient in the film-substrate system generates a greater wafer bow and residual stress in the grown thin film. Therefore, temperature uniformity is an important parameter for the epitaxial process. The sign of residual stress is different between a GaN film grown on a sapphire wafer and a silicon wafer (compressive for sapphire wafer and tensile for silicon wafer). For growing a GaN thin film, sapphire wafer is better than silicon wafer in terms of lessening cracking in film.