Silicon-based materials have been used in electronic microfluidic devices. The heat dissipation effect has become an important index to evaluate their performance, so different process methods have been applied to the patterning processing of silicon-based materials to enhance the heat dissipation performance. The laser etching was used to machine microgrooves on the surface of Si samples in this research. To reduce the thermal influence of laser processing on silicon materials, the ultrashort pulse laser with a pulse width of 12 ps was used to process microgrooves, during which the influence of laser processing parameters such as different laser power and laser scanning times on microgrooves was analyzed. With the help of laser confocal microscopy, the effects of different laser parameters on the depth and roughness of the bottom of the microgroove were studied. The results showed that increasing the laser power and the number of laser scans could effectively increase the depth and roughness of microgroove.