Microchannel heat dissipation systems are widely used in micro-electro mechanical systems owing to their high thermal conductivity and small size. Laser processing has the advantages of high efficiency and no tool contact, and is one of the best ways to process ceramic materials. However, the roughness of the machined surface will significantly affect the heat dissipation performance of the microchannel. In order to study the influence of roughness element characteristics on the heat dissipation efficiency of the micro-channel radiator, the surface roughness was simulated with typical shape, and the influence of different roughness element shape, height and spacing on the pressure field, velocity field and temperature field of the micro-channel radiator was analysed. The results indicate that the semi-circular roughness element has the highest heat transfer efficiency and that the overall flow is stable. With an increase in the height of the roughness element and a reduction in the spacing, the heat transfer efficiency and inlet/outlet pressure drop increased. When the height of the roughness element is 17.2 μm, the heat transfer ability was significantly improved and the pressure drop ratio is reduced by >20% compared with that for a height of 19.5 μm. When the distance between roughness elements is 33.5 μm, the maximum temperature of the heat dissipation system was only 331.85 K. Compared with other models, the temperature of the optimized model is reduced by 14.44K, and the heat transfer efficiency is the highest. The results of heat dissipation experiments show that compared with dry burning temperature, the optimized model can reduce the temperature of the micro-channel heat dissipation system by more than 73 K.