A method considering thermal boundary conditions and thermal coupling effects is proposed to estimate the junction temperature of double-sided cooling insulated-gate bipolar transistor (IGBT) modules. Traditional methods, which rely on negative temperature coefficient (NTC) measurements, often overlook mutual thermal interactions among chips, leading to inaccuracies under varying cooling boundary conditions. In this paper, a Foster thermal network model incorporating chip thermal coupling is developed to estimate the junction temperature of double-sided cooling IGBT power modules. The thermal model parameters are extracted through a combination of finite element simulation and experimental analysis. The effects of different cooling boundary conditions on the thermal model and the module’s heat channeling behavior are examined, and compensation strategies for various cooling boundaries are proposed. Experimental and simulation results indicate that the estimated junction temperature error of the proposed method remains within 5 °C under different operating conditions.