The heat exchanger is widely applied to many axial piston machines, and its structure significantly affects the heat transfer performance. Flow characteristic and heat transfer performance in heat exchanger channels with different dimples geometries are numerically and experimentally analyzed in this research work. The objective is to present details of flow field structure and heat transfer mechanisms for the dimpled channel. The realizable k-ε turbulence model was employed in the numerical simulations with the Re range from 3500 to 20,000. The temperature contour, local streamlines, friction factor, and Nu were presented to illustrate the heat transfer enhancement mechanisms. From this investigation, it is found that dimples cause downward flow, improve the flow mixing and reattachment, interrupt the boundary layer and form periodic impingement flows and then greatly improve the heat transfer. The heat transfer coefficient of hemispherical dimple channels with the three kinds of dimple radius–depth ratios is the highest, and it is about 27.2% higher than that of the traditional rhombus dimple channel. Comparing to the rhombus dimpled channel, the lower flow friction performance of the hemispherical dimple channel depends on the lower dimple radius–depth ratio. The hemispherical dimpled channel present better overall thermal performance due to the strength and extent of the recirculation flow reduction.