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Scroll compressors are commonly used in HVAC and thermal management systems of electric and hybrid vehicles because of its high operating efficiency and smooth operation. The compressor is driven by an electric motor which forms a coupled system called an e-compressor unit. The refrigerant cools the motor before entering the scroll compressor. At different operating conditions of the vehicle, the change in power of the motor alters the refrigerant temperature and hence affecting the compressor’s performance. In the present work, 3D Conjugate Heat Transfer simulation of an e-compressor is performed as a complete unit with flow and heat transfer through the motor and compressor. A novel mixed timescale approach for the heat transfer has been developed to simulate the effect of thermal loads on the performance of the compressor. These performance parameters include the outlet temperature, volumetric efficiency, and discharge flow rate of the compressor.