A test system and method for thermoelectric module. The test system includes an electrical performance test unit, a heat flux detection unit, and a processor. The electrical performance test unit connects with the thermoelectric module under power generation state to test output power of the thermoelectric module and working current and internal resistance under this output power. The heat flux detection unit includes a heat flux sensor installed at a cold-end of the thermoelectric module to detect the heat flux. The processor electrically connects with the electrical performance test unit and the heat flux detection unit to calculate the thermoelectric conversion efficiency η of thermoelectric module. By using the technical scheme of the invention, the detection of the thermoelectric conversion efficiency of the thermoelectric module is accomplished.