High silica glass fiber is widely used and has the superior properties. Acid leaching is the main existing method to prepare high silica special glass fiber. In this paper, high silica glass fiber was prepared via acid leaching and heat treatment. The structure of SiO2-Na2O binary glass fiber during acid leaching and heat treatment was investigated by Raman spectroscopy. The results show that the bending vibration peak and asymmetric stretching vibration peak shift to a lower wavenumber, and the peak intensity becomes weaker during acid leaching process, mainly because SiO2 content in the fiber increases and the internal structure of the fiber changes to a chain structure. After heat treatment, the asymmetric stretching vibration peaks disappear, and the defect lines D1 and D2 appear, and the density of fibers changes at different heat treatment temperatures, mainly due to the condensation reaction of fiber during heat treatment.