Fused quartz glass is widely used in the civil and national defense fields. Shear-thickening polishing (STP) technology is highly efficient for processing quartz glass. However, the surface and subsurface damage (SSD) caused by STP have yet to be studied. In this study, the SSD characteristics of quartz glass after STP were examined using chemical etching and nanoindentation tests. The Sa (average roughness) of the fused quartz glass after 30 min of STP was 1.6 nm and the embedded depth of impurities was approximately 30 nm. The 3D morphology of the Beilby layer was sensitive to the chemical etching time, disappearing when the etching time was 120 s (at which point the Beilby layer with a depth ranging from 97 to 144 nm was completely removed). From various analysis methods, it can be inferred that the SSD depth was between 4.8–6.7 µm. To confirm that the above SSD came from the grinding or STP process, the polished fused silica glass was etched for 150 min to remove the SSD, after which it was polished for 30 min to regain its smooth surface; the workpieces were then etched again and the Sa and 3D morphology were compared with the workpiece which had no damage removal. The results showed that STP did not introduce new SSD and was a near-lossless polishing technique under the conditions used in this study. STP can achieve an extremely low surface roughness, efficiently; however, the depth of material removal is insufficient, and the SSD caused by the grinding process remains.