Epidermal electronic systems (EESs) are a representative achievement for utilizing the full advantages of ultra-thin, stretchable and conformal attachment of flexible electronics, and are extremely suitable for integration with human physiological systems, especially in medical hyperthermia. The stretchable heater with stable electrical characteristics and a uniform temperature field is an irreplaceable core component. The inorganic stretchable heater has the advantage of maintaining stable electrical characteristics under tensile deformation. However, the space between the patterned electrodes that provides tensile properties causes uneven distribution of the temperature field. Aiming at improving the temperature distribution uniformity of stretchable thermotherapy electrodes, an orthotropic heat transfer substrate for stretchable heaters is proposed in this paper. An analytical model for transient heat conduction of stretchable rectangular heaters based on orthotropic transfer characteristics is established, which is validated by finite element analysis (FEA). The homogenization effect of orthotropic heat transfer characteristics on temperature distribution and its evolutionary relationship with time are investigated based on this model. This study will provide beneficial help for the temperature distribution homogenization design of stretchable heaters and the exploration of its transient heat transfer mechanism.