As electronics become more powerful and compact, laminated microchannel heat sinks (MCHSs) are essential for handling high heat flux. This study aims to optimize the MCHS design for improved heat dissipation and structural strength. An orthogonal experiment was established with the average surface temperature of the heat source as the evaluation metric, and the optimal structure was determined through simulation. Finally, cooling uniformity, fluidity, and performance evaluation criterion (PEC) analyses were carried out on the optimal structure. It was determined that the optimal combination was the triangular cavity microchannel (MCTC), with a microchannel width of 0.5 mm, a microchannel distribution density of 60%, and the presence of surface undulation on the microchannels. The result shows that the optimal structure’s peak inter-layer stress is just 34.8% of its longitudinal tensile strength. Compared to the traditional parallel straight microchannel (MCPS), this structure boasts an 8.6 K decrease in the average surface temperature and a temperature variation along specific paths that is only 9.9% of that in traditional designs. Moreover, the optimal design cuts the velocity loss at the microchannel entrance from 75% to 59%. Thus, this research successfully develops an effective optimization strategy for MCHSs.