The manifold microchannel (MMC) heat sink system has been widely used in high-heat-flux chip thermal management due to its high surface-to-volume ratio. Two-phase, three-dimensional numerical methods for subcooled flow boiling have been developed using a self-programming solver based on OpenFOAM. Four different types of manifold arrangements (Z-type, C-type, H-type and U-type) have been investigated at a fixed operational condition. The numerical results evaluate the effects of flow maldistribution caused by different manifold configurations. Before simulating the two-phase boiling flow in MIMC metamodels, single-phase liquid flow fields are performed at first to compare the flow maldistribution in microchannels. It can be concluded from the flow patterns that H-type and U-type manifolds provide a more even and a lower microchannel void fraction, which is conducive to improving the temperature uniformity and decreasing the effective thermal resistance. The simulation results also show that the wall temperature difference of H-type (0.471 K) is only about 10% of the Z-type (4.683 K). In addition, the U-type manifold configuration show the lowest average pressure drop at the inlet and outlet of the MIMC metamodel domain. However, H-type manifold also shows an impressive 59.9% decrease in pressure loss. Results indicate that both the H-type and the U-type manifolds for flow boiling in microchannels are recommended due to their better heat transfer performance and lower pressure drop when compared with Z-type and C-type.