This study analyzes heat transfer effects inside vacuum packaged microelectromechanical system (MEMS) devices. A packaged device is simplified as four plates forming a square cavity, the bottom plate represents a hot chip, while the other three plates are maintained at room temperature. For a highly rarefied free molecular internal gas flow scenario, the corresponding detailed density and temperature fields are analytically determined with a proposed speculation. This speculation indicates that for a steady free molecular gas flow inside a convex closure domain formed by walls maintained at different temperatures: (1) the velocity distribution functions for those molecules diffusely reflected at different walls and traveling away from them are Maxwellian with different number densities; (2) for each distribution, niTi is a constant, where ni is the number density for the group of reflected molecules, and Ti is the temperature for the ith plate. For a near continuum flow scenario, the governing energy equation degenerates to Laplace’s equation with several temperature-jump wall boundary conditions. This study also includes discussions and comparisons among analytical results, simulation results from the direct simulation Monte Carlo method, and results by solving the Navier–Stokes equations with proper wall boundary conditions. The approach used in this study is generally applicable to study internal flows and heat transfer effects in other vacuum packaged MEMS devices with different shapes.