It is necessary to control the temperature of solar cells for enhancing efficiency with increasing concentrations of multiple photovoltaic systems. A heterogeneous two-phase model was established after considering the interacting between temperature, viscosity, the flow of nanofluid, and the motion of nanoparticles in the nanofluid, in order to study the microchannel heat sink (MCHS) using Al2O3-water nanofluid as coolant in the photovoltaic system. Numerical simulations were carried out to investigate the thermal performance of MCHS with a series of trapezoidal grooves. The numerical results showed us that, (1) better thermal performance of MCSH using nanofluid can be achieved from a heterogeneous two-phase model than that from single-phase model; (2) The effects of flow field, volume fraction, nanoparticle size on the heat transfer enhancement in MCHS were interpreted by a non-dimensional parameter NBT (i.e., ratio of Brownian diffusion and thermophoretic diffusion). In addition, the geometrical parameters of MCHS and the physical parameters of the nanofluid were optimized. This can provide a sound foundation for the design of MCHS.