Microchannels fabricated by femtosecond laser-assisted chemical etching are of great use in biochemical analysis. In this paper, we study the morphology change of etched microchannels in fused silica by controlling the laser scan speed, and we find a significant difference between the chemical etched length and volume. The fabricated microchannels would gradually become tapered along the scan direction, which influences the flow of the hydrofluoric (HF) reagent and the etching rate. As a result, the difference ratios of the etched length and volume, respectively, reach -5.56% and -41.83% followed by the scan speed increasing from 5 to 200 µm/s. Microchannels with polarization independence and better aspect ratio could be obtained in a high-speed-scan mode. We suggest that laser-induced structural transformation from interconnected microcracks to nanogratings could be responsible for this change. Aforementioned results offer a feasible approach to achieve polarization-independent microchannels, which is in favor of accelerating the fabrication of three-dimensional microfluidic devices.