A model of rectangular microchannel heat sink (MCHS) with porous medium (PM) is developed. Aspect ratio of heat sink (HS) cell and length-width ratio of HS are optimized by numerical simulation method for entropy generation minimization (EGM) according to constructal theory. The effects of inlet Reynolds number (Re) of coolant, heat flux on bottom, porosity and volume proportion of PM on dimensionless entropy generation rate (DEGR) are analyzed. From the results, there are optimal aspect ratios to minimize DEGR. Given the initial condition, DEGR is 33.10% lower than its initial value after the aspect ratio is optimized. With the increase of Re, the optimal aspect ratio declines, and the minimum DEGR drops as well. DEGR gets larger and the optimal aspect ratio remains constant with the increasing of heat flux on bottom. For the different volume proportion of PM, the optimal aspect ratios are diverse, but the minimum DEGR almost stays unchanged. The twice minimized DEGR, which results from aspect ratio and length-width ratio optimized simultaneously, is 10.70% lower than the once minimized DEGR. For a rectangular bottom, a lower DEGR can be reached by choosing the proper direction of fluid flow.