In typical gas-to-liquid thermoelectric generators for waste heat recovery, the stream-wise gas temperature drop in the hot-side heat exchanger leads to the decrease of power output of the whole system. Denser fins are usually arranged on the downstream of the hot-side heat exchanger to improve the uniformity of temperature field and thus the total power output performance of thermoelectric generators when the steam-wise temperature drop is small, but it is not benificial when the steam-wise temperature drop is large. This work investigates the effect of configuration of winglet vortex generators on the performance of thermoelectric generator system. Three sets of hot-side heat exchangers, including a heat exchanger with smooth channel, a heat exchanger with uniform configuration of winglet vortex generators and a heat exchanger with non-uniform configuration of winglet vortex generators, are tested in a gas-to-liquid thermoelectric generators experimental system. The hot-side Reynolds number ranges from 3000 to 6400 and the hot-side inlet temperature is within 523-553 K. The experimental results show that the total and net power output of thermoelectric generator under matched load resistance with uniform heat exchanger can respectively outperform that with smooth heat exchanger by 97.5% and 77.7% in average, whereas that with non-uniform heat exchanger by 189.1% and 177.4% in average. Since the uniform and non-uniform heat exchangers have the same number but different configuration of winglet vortex generators, this kind of active cascade control of heat transfer enhancement elements is proved to be effective in improving the power output of thermoelectric generator system without increasing pumping power.