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In this paper, the different heat source distributions are studied in the micro-channel heat sink (MCHS) cooler. The simulation model is established to analyze the heat distributing and temperature rise of the MCHS with different channel width-dimensions. Uniform and non-uniform heat source are used to offer a constant heat flux, and the total heat flux amount is 270 W. Water is chosen as the coolant for its superior hot properties and the velocity range is from 0.01 m/s to 10 m/s. The results show that tradition type MCHS will be under a low efficiency for cooling a non-uniform heat source. And the non-equal displacement of fins can effective decrease the temperature rise about 10% under the same cooling conditions cooling a non-uniform heat source. We also find that it is impossible to enhance the cooling effect through adding the flow rate if it has surpassed itpsilas limitation.