β-quartz is an important component that affects the physical and chemical properties of glass-ceramics. The material removal process of ion beam machining is complicated as one of the ultra-precision machining forms. Therefore, it is important to understand the removal mechanism of ion beam machining materials. The methods of molecular dynamics (MD) and first-principles were adopted to investigate the microscopic mechanism of ion beam bombardment of the β-quartz structure. The damage evolution of structures and the evolution of material properties caused by defects respectively from the atomic and electronic levels. Through MD analysis, we find that the random collision between incident ions and matrix atoms can lead to the formation of sputtered atoms. The incidence of ions will increase the disorder degree of the matrix, and the influence on the disorder degree at different depths of the matrix is different. The degree of disorder increases obviously in the range of 50–70 Å from the surface of the matrix. It has a significant impact on the surface topology of the matrix, the number of defects, surface roughness, and matrix density. The results of first-principle calculation show that the refraction, absorption and other characteristics of the system are significantly different with different doping forms, and the energy loss is most affected by substituted doping. And the substituted doping defects have the most significant effects on the structural energy loss. Among, the Ar-substituted O doping structure leads to higher energy loss, and the peak energy loss intensity reaches 5.146. In contrast, the Ar-substituted Si doping structure causes the least energy loss, the intensity is 2.543. This study provides a theoretical basis for the selection of parameters and the realization of ultra-smooth surface in actual ion beam machining.