As for improving the heat diversion capacity of the hot side heat sink of the thermoelectric cooler (TEC), thereby improving the operational performance of the TEC, this study designed a type of double‐embedded flat heat pipe (EFHP) finned heat sink and compared with a standard aluminum (Al) heat sink. In experimental studies, TEC under two heat sinks were placed under different operating currents for heat transfer analysis and performance comparison. The experimental results demonstrated that the EFHP heat sink had better heat diversion ability, effectively improving the operational performance of TEC. When the TEC was input with a current of 6A, the thermal resistance of the double EFHP finned heat sink decreased by 19% compared to the Al heat sink; cooling capacity and coefficient of performance increased by 8.3% and 9.46%, respectively. Further, TEC's cold and hot surface temperatures decreased by 10.83% and 10.2%, respectively, and the heat uniformity of the heat sink improved. In addition, the CFD software Icepak was used to analyze the effects of double flat heat pipe spacing and length on the heat sink and TEC and the performance of two heat sinks and TEC under different heat dissipation conditions and obtained good agreement. This study can provide further guidance and assistance in designing the TEC cooling system.