Microchannel heat sink shape optimization is performed using Kriging method. Design variables relating to microchannel width, depth and fin width are selected, and thermal resistance has been taken as objective function. Design points are selected through a three-level fractional factorial design of sampling method. Navier-Stokes and energy equations for laminar flow and conjugate heat transfer are solved at these design points using a finite volume solver. Solutions are carefully validated with experimental results. Using the numerically evaluated objective function, a surrogate model (Kriging) is constructed and optimum point is searched by sequential quadratic programming. The process of shape optimization greatly improves the thermal performance of microchannel heat sink under constant pumping power.