The manifold microchannel heat sink receives an increasing number of attention lately due to its high heat flux dissipation. Numerical investigation of boiling phenomena in manifold microchannel (MMC) heat sinks remains a challenge due to the complexity of fluid route and the limitation of numerical accuracy. In this study, a computational fluid dynamics (CFD) approach including subcooled two-phase flow boiling process and conjugate heat transfer effect is performed using a MMC unit cell model. Different from steady-state single phase prediction in MMC heat sink, this type of modeling allows for the transient simulation for two-phase interface evolution during the boiling process. A validation case is conducted to validate the heat transfer phenomenon among three phases. Besides, this model is used for the assessment of the manifold dimensions in terms of inlet and outlet widths at the mass flux of 1300 kg/m2·s. With different ratios of inlet-to-outlet area, the thermal resistances remain nearly stable.