Higher heat flux is produced by Micro-Electro-Mechanical Systems (MEMS) because of their reduced size and increased clock speed. At the mean time, studies of non-uniform heating conditions which are more practical than uniform heating conditions are inadequate and needed urgently. Four nonuniform heating conditions are simulated in the paper. Three heat sinks with different widths of cross-linked channels locating above the center of hotspots are studied and compared to conventional straight microchannel heat sink. Half of the module geometry is chosen to be the computational domain. Two hotspots are placed at the bottom surface. The coolant is water, whose properties are dependent on temperature. Two inlet velocities, 0.5 m/s and 1 m/s, are tested for each heat sink. Temperature profile at the hotspots, pressure drop and total thermal resistance are selected as criteria of evaluating heat sink performance. All heat sinks have better performance when there is an upstream hotspot or the upstream hotspot is subjected to a higher heat flux. Cross-linked channel width of 0.5 mm has the best benefit to obtain better temperature uniformity without increasing the maximum temperature on the bottom surface.