Spin-transfer-torque magnetic random access memory (STT-MRAM) based on magnetic tunnel junction (MTJ) device has attracted significant attention from academics and industries. Nevertheless, the thermal effect under bias operation affects the overall performance and stability of a device. To evaluate the thermal phenomenon in MTJ devices accurately, the non-equilibrium effect between the electron and the phonon near the electrode-barrier interface cannot be ignored. The existence of the interface leads to additional thermal resistance hindering the heat conduction of tunnel junction. Therefore, an effective equivalent model concerning the interface effect is necessary to represent the heat transportation of the device. In this article, a nanoscale thermal transport model of the MTJ device is proposed. The influence of the thermal conductivity of the nano-oxide layer on the temperature distribution is discussed. The interface energy balance transport model is used to clarify the non-equilibrium relationship between the phonon and the electron at the CoFeB/MgO/CoFeB interfaces. A parameterization study is conducted to illustrate the temperature distribution in the nanoscale thermal transport model. Furthermore, the phonon-electron coupling distance ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\delta$ </tex-math></inline-formula> ) based on the thermal conductivity of the phonon ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\kappa _{p}$ </tex-math></inline-formula> ) and the electron ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\kappa _{e}$ </tex-math></inline-formula> ) of the device is implemented to construct the effective equivalent model using finite element modeling (FEM), which could realistically reflect the thermal transport under working conditions. The established equivalent model has a guiding role in exploring the thermal transportation in the nanoscale MTJ device.