Based on conductive cooled slab laser amplifiers with end-pumping structure, a rectangular micro-channel water cooling heatsink as the amplifier cooling system has been designed. Optimization of the micro-channel heatsink was investigated by the finite element analysis (FEA) , which showed that the cooling performance is the best when the ratio of width of microfin valley to width of microchannel is 0.57. Comparing the experiment with the simulation of a micro-channel heatsink with 0.4 mm width of microfin valley and 0.35 mm width of microfin, the curve of heat transfer coefficient and water flow rate was fitted, resultant temperature distribution of the laser slab under cooling of the heatsink was obtained by FEA. Results indicated that low thermal resistance in the slab cooling surface was obtained even the water flow rate was slow.