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A three-dimensional convective heat transfer model of a microchannel pin-fin hybrid heat sink was established. Considering the non-uniform heat generation of 3D stacked chips, the splitting distance of pin-fins was optimized by minimizing the maximum heat sink temperature under different heat fluxes in the hotspot, the Reynolds numbers at the entrance of the microchannel, and the proportions of the pin-fin volume. The average pressure drop and the performance evaluation criteria were considered to be the performance indexes to analyze the influence of each parameter on the flow performance and comprehensive performance, respectively. The results showed that the maximum temperature of the hybrid heat sink attained a minimum value with an increase in the splitting distance. The average pressure drop in the center passage of the microchannel first increased and then decreased. Furthermore, the optimal value could not be simultaneously obtained with the maximum temperature. Therefore, it should be comprehensively considered in the optimization design. The heat flux in the hotspot was positively correlated with the maximum heat sink temperature. However, it had no effect on the flow pressure drop. When the Reynolds number and the pin-fin diameter increased, the maximum heat sink temperature decreased and the average pressure drop of the microchannel increased. The comprehensive performance of the hybrid heat sink was not good at small Reynolds numbers, but it significantly improved as the Reynolds number gradually increased. Choosing a bigger pin-fin diameter and the corresponding optimal value of the splitting distance in a given Reynolds number would further improve the comprehensive performance of a hybrid heat sink.