In this paper, laminar forced convection heat transfer of water-Al2O3 and water-Cu nanofluids in a double-layered microchannel heat sink is studied numerically. To simulate the heat transfer in the double-layered microchannel heat sink, two phase mixture model is used. In this method, continuity, momentum, energy and void fraction equations are solved for steady state, incompressible and three dimensional flow, using the finite volume method (FVM). The Brownian motion effect is considered in determining the effective thermal conductivity that also depends on the nanofluid temperature. Numerical modeling is done for different nanoparticle volume fractions, nanoparticle diameters and Reynolds numbers. The calculated results show that increasing the nanoparticle volume fraction and Reynolds number increases the Nusselt number. Also, an increase in the nanoparticle diameter, increases the pressure drop slightly and decreases the Nusselt number. As an example, for water-Al2O3 nanofluid at Re = 500 and with 0.05 nanoparticle volume fraction with 80 and 100 nm particle diameters, the enhancement in Nusselt number compared to the pure water is 20.32% and 20.21% respectively. Furthermore, the performance of water-Al2O3 and water-Cu nanofluids in a constant volumetric flow rate is compared. According to this comparison, maximum Nusselt number and pressure drop belongs to water-Cu nanofluid.