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The superhydrophobic silica glass microchannel with flow drag reduction performance has broad application prospects. In response to this demand, this paper proposes an integrated design and preparation method of structure and function for drag reduction microchannels on the silica glass surface. The design method of geometric parameters of stable superhydrophobic silica glass surface structures with a periodic micropillar array is studied based on the drag reduction mechanism of superhydrophobic surfaces. Combined with the plasma deposition process, the drag-reducing superhydrophobic silica glass surface is successfully prepared by femtosecond laser technology. The prepared drag-reducing superhydrophobic silica glass surface shows good composite wetting state stability under different test conditions. The drag-reducing superhydrophobic functional structure with a micropillar array is prepared at the bottom of the silica glass microchannels by femtosecond laser direct writing technology. Moreover, the effective integration of the silica glass microchannel structure and the drag-reducing functional structure is achieved. The preparation and flow performance test of microfluidic devices demonstrates that drag-reduction microchannels of silica glass can significantly reduce microfluidic flow resistance. The proposed method effectively improves the functional characteristics of ultrafast laser processing surface microchannels in silica glass and has broad application prospects in fluid flow and control.