Dimple on the surface is widely used in electronic cooling equipment, turbine blades, and combustion chamber gaskets and so on, which is a good structure for heat transfer enhancement. In this paper, taking comprehensive performance parameters of flow and heat transfer PEC as an evaluation parameter, numerical simulation, and multi-island genetic algorithm are combined to optimize the shape of the dimple in microchannel under fully developed laminar condition. The results show that the optimal dimple is asymmetric along the flow direction, and the deepest position of which shifts downstream, which is dependent on the Reynolds number, the dimple diameter, and the periodic length. With the increase of the Reynolds number and the dimple diameter, the Nusselt number ratio, the Fanning fraction factor ratio, and the comprehensive performance parameter PEC increase for the optimal dimple. The separation of the fluid in the front edge of dimple is not conducive to heat transfer. The number and size of the vortex, the impact, and the reattachment are found to be the key factors affecting the heat transfer in the dimple. As the periodic length L of the heat transfer unit decreases, the heat transfer is enhanced and the flow resistance increases, and the comprehensive performance of the microchannel becomes better.