For vehicle thermoelectric generator, heat would be directly transferred into electricity by thermoelectric modules because there was temperature difference between heat exchanger and water tank. The electrical power generation was deeply influenced by temperature difference, temperature uniformity and topological structure of TEG. In previous works, increasing the difference of temperature would significantly enhance the power generation of TEG and inserted fins were always applied to enhance heat transfer in parallel-plate heat exchanger. But fins would result in a large backpressure which was not conductive to efficiency of the engine.In current study, to enhance heat transfer rates and outside surface temperature, cylindrical grooves on the top and bottom surface in heat exchanger was proposed. The cylindrical grooves could increase the heat transfer area and enhance the turbulence intensity, meanwhile there was no inserts in the fluid to block the flow. In the themoelctric generator systems, the flow direction in heat exchanger was opposite to that in water tank. And the surface temperature of water tank and heat exchanger with three internal structures, such as groove surface (the depth-to-width ratio is 0.25 ), flat surface and inserted fins, was studied by numerical investigation at different rows of thermoelectric modules. The efficiency of TEG in terms of power generation and backpressure were compared based on the simulation. The results showed that comparing to other structures, heat exchanger with cylindrical grooves could improve the efficiency of TEG at a low backpressure. Finally a heat exchanger with relatively ideal performance in TEG was obtained.