Abstract: Glass microchannels with inner surfaces of different wettabilities and roughnesses were obtained through modification by hydroxylation treatment to achieve hydrophilic surfaces，by self-assembly of chlorotrimethylsilane to achieve hydrophobic surfaces，and by sol-gel SiO2 nanoparticle deposition to generate rough surfaces. Effects of the inner surface properties of microchannels on the fluid flow characteristics therein have been systematically investigated. When the inner surfaces of microchannels are of the same wettability (hydrophilic or hydrophobic)，the resistance of rough surfaces to the fluid flow in the microchannel is larger than that of smooth surfaces，and such effect is more significant when the fluid flows faster. When the inner surfaces of microchannels are of the same roughness，the resistance of hydrophobic surfaces to the fluid flow in the microchannel is larger than that of hydrophilic surfaces，and such effect is also more significant when the fluid flows faster. In comparison，the effect of wettability of the inner surfaces of microchannel on fluid flow therein is larger than that of roughness. These results provide valuable guidance for the design and application of micro-flow system and micro-fluid machinery.