In order to improve the heat transfer efficiency and the performance of the thermoelectric microwave power sensors, the substrate structure of the thermoelectric microwave power sensors was optimized, and the optimal substrate structure size was obtained in this work. Firstly, the influence of substrate thickness on thermoelectric microwave power sensors was studied. Then, according to the obtained optimal substrate thickness, the effects of substrate position and size on the performance of thermoelectric microwave power sensor were studied. Finally, the microwave characteristics and electromagnetic field distribution of the sensor with the optimal substrate structure were studied. The results show that when the structure size of the sensor substrate is optimal, the maximum temperature of the sensor reaches 352.76 K and the S parameter is less than -20.62 dB. The structure not only reduces the heat dissipation in the substrate and improves the heat transfer efficiency from the load resistance to the thermopile, but also has good microwave characteristics.