Microchannel heat sink is fabricated on silicon wafer by anisotropic etching, and used Pyrex #7740 as a transparent cover that integrated by anodic bonding. Rectangular microchannel presents the flow phenomena of fluid in micro scale, and this study focus on the boundary conditions which hydraulic diameter (Dh) is from 80m to 350m and Aspect ratio is from 0.24~7.8 of working fluid (DI water). While the size of microchannel is decreasing, laminar flow occurs on the low Reynolds number, which caused by the interaction of viscosity and friction on boundary layer. Sequentially, the influence of dimension decreasing on microchannel that induced transition and turbulent flow in early stage as Reynolds number is still in the range of 600~800. Pressure drop is high (2 bar) when fluid flows through the micro channel, and flux is constrained by the flow resistance during experiment operating. In this study, it takes effect by increasing aspect ratio to reduce pressure drop and enlarge the conductive surface. Geometry of microchannel, hydraulic diameter, and aspect ratio are the key factors in flow phenomena investigation. This research presents the difference between micro scale flow and traditional pipe flow by consideration of Reynolds number. By using computer aided engineering to optimize the aspect ratio of microchannel, which can find the maximum conductive surface under the limitation of pressure drop. The best value of aspect ratio is 0.88~1.22. The simulation result makes good sequence with experiment data. Based on this methodology, numerical analysis can be used to design the optimal microchannel on wafer for cooling hot spot.