The flat Loop Heat Pipe (LHP) has the advantages of small size, light weight, and direct contact with the heat source without additional thermal resistance, which has gradually drawn attention and importance in the aerospace field. However, for the vertically arranged flat LHP, there is a significant amount of reverse heat leakage from the evaporator to the compensation chamber, resulting in a low operating efficiency of the heat pipe. This paper proposes a thermal control structure coupling the flat LHP with thermoelectric cooler (TEC), which investigates the effects of TEC on the start-up speed, working temperature, system thermal resistance, temperature fluctuation, and reverse temperature control of the flat LHP through experimental studies. The results show that the TEC can help improve the start-up speed of the heat pipe by approximately 50 % under low heat load. The heat resistance of the LHP is greatly reduced to approximately 0.13–0.15 °C/W, and the working temperature curve changes from “V” type to a linear line with increasing heat load power. Moreover, by using the TEC to provide reverse power to the compensation chamber for temperature control, the temperature control efficiency is extremely high, and a temperature rise of approximately 10 °C can be achieved with only 0.1 W TEC power. The above research indicates that the TEC can significantly weaken the disadvantage of the flat LHP and improve its engineering practicality.