Due to the compact layout, the design space for motor controller in electric vehicle is limited. Besides, fan cooling is forbidden in some cases to ensure the reliability of the motor controller and the highpower chips. In order to decrease the temperature of highpower chips in motor controller, structural optimizations are carried out. Firstly, layout of the chips is rearranged to change the surrounding flow field. Secondly, structure of the printed circuit board (PCB) is changed to alter the flow field. Finally, the cold end heat conduction structure is used to cool the chips. The optimization measures are verified by simulation. The optimization results can provide theoretical guidance for the heat dissipation design of the motor controller.