For the safe and stable operation of electronic equipment, the corresponding cooling technology should achieve not only the removal of ultra-high heat flux, but also the uniformity of temperature distribution. The heat transfer performance of the heat sink mainly depends on the flow distribution inside. For this reason, the distribution of flows is a more critical issue. In the interdigitated microstructures, the manifolds are mainly used to uniform the flow distribution of the heat sinks. In this research, the manifold layers are optimized primarily through the number of manifolds layers, and the manifold size. Furthermore, a comparative study between manifold microchannel (MMC) and manifold micro-pin-fin (MMPF) is also investigated. The uniformity index of temperature is the main parameter introduced to evaluate the temperature distribution on the heated wall. The results show that the optimal design of the manifold influenced the thermal and hydrodynamic performance, which can significantly improve the temperature uniformity on the heated wall. However, the pressure drop of the heat sink is also multiplied for the multi-layer manifold design because of the more complex structure design. The 3 layers manifold heat sink reaches the best flow distribution since the pressure distribution is the most uniform in the microstructures. However, the flow direction in the third manifold layer is vertical to the microchannels, which decreases the heat transfer performance of MMC. The 2 layers MMC heat sink performs the lowest total thermal resistance of 0.088×10^-4 Km²/W. However, the 3 layers MMPF heat sink achieves the lowest total thermal resistance of 0.085×10^-4 Km²/W. The MMPF heat sink shows more potential in uniform heat dissipation.