Microchannel heat sinks have been widely used in high-density packaged electronic device cooling technology. We combined the cantor fractal structure with the microchannel heat sink to design a new type of microchannel structure. Combining fractal structure with microchannel heat sink is one of the cutting-edge technologies of heat transfer to solve the heat dissipation problem of high heat flux electronic equipment. We chose the width-to-height ratio of the microchannel inlet (a/b), the width-to-height ratio of the Cantor fractal baffle (B/h) and the ratio of the microchannel inlet width and the distance between each group of baffles (a/λ) as design variables, and the optimization objective was to make the global thermal resistance and pump work minimum. First, the pressure drops, temperature, and velocity of the microchannel heat sink were analyzed. Then, to consider the fluid heat transfer and pressure drop comprehensively, the enhanced heat transfer factor PEC was used to evaluate the comprehensive heat transfer performance of the microchannel. The final optimized structure PEC values were all greater than 1. In the Reynolds number (Re) range of 100-500, its enhanced heat transfer factor PEC is 1.56-1.79, which indicates that the heat transfer effect of the optimized microchannel heat sink is greatly enhanced than that of the conventional microchannel.