In order to improve the morphology of microchannels fabricated by femtosecond laser ablation, the thermal process was introduced into the post-treatment processing. It was found that the thermal process cannot only decrease the roughness but also the width and depth of the microchannel. The change rates of width, depth, and roughness of the microchannel increase with processing temperature. When we prolong the time of constant temperature, the change rate of the width decreases at the beginning, and then it tends to be stable. However, the change rates of depth and roughness increase, and then they tend to be stable. In this Letter, we discuss the reasons of the above phenomena.