This research will focus on studying the effect of aperture size and shape of the micro-channel heat sink on heat dissipation performance for chip cooling. The micro-channel heat sink is considered to be a porous medium with fluid subject inter-facial convection. Derivation based on energy equation gives a set of governing partial differential equations describing the heat transfer through the micro-channels. Numerical simulation, including steady-state thermal analysis based on CFD software, is used to create a finite element solver to tackle the derived partial differential equations with properly defined boundary conditions related to temperature. After simulating three types of heat sinks with various protrusion designs including micro-channels fins, curly micro-channels fins, and Micro-pin fins, the result shows that the heat sink with the maximum contact area per unit volume will have the best heat dissipation performance, we will interpret the result by using the volume averaging theorem on the porous medium model of the heat sink.