To obtain a smooth surface of etched-fiber core, a flow etching system was developed based on mass-transfer and dynamic response characteristics in silica optical fiber etching processes. The effects of fiber composition, etchant temperature and flow rate on the etching rate of fibers and the surface morphology of etched-fibers were investigated in the mass percent concentration of Hydrofluoric Acid (HFA) at 12.5%, respectively. The experimental and theoretical studies show that the etching rate and the surface roughness of the etched-fibers are controlled by the chemical reaction rate and mass transfer rate. The etching rate of fiber core is higher than that of fiber cladding because of the compositional difference between the fiber core and fiber cladding. In the static etching condition, the increase of the etching rate is nonlinear with temperature, and the etched-fiber gives a rough surface.Moreover,in the flow etching condition, the etching rate is improved and is linear with temperature, and the roughness of the etched-fiber core increases at first and then decreases with the increase of etchant flow rate. The results also show that the etched-fiber core with smooth surfaces can be repeatedly obtained with the etchant flow rate at 0.75 L/min.