Wet etching of quartz is an important microfabrication technique for etching and patterning structures by etching material surfaces using liquid chemicals. However, because of its complex anisotropy, it leads to the simulation of etching results that are often difficult to predict and control. In this paper, we propose a new modeling method based on Monte Carlo method to calculate the offset between quartz atom crystal cells and an atomic code to quickly determine the characteristic attributes around each atom, which reduces the amount of calculation and calculation time of the algorithm compared to the traditional modeling method by avoiding a large number of computational processes in modeling and the need to traverse all the other atoms to determine the configuration state of the target atoms after the completion of the modeling. At the same time, the modeling method is more in line with the actual microstructure of quartz crystals, which is more suitable for the basic modeling of quartz crystal etching simulation, and can theoretically better simulate the etching behavior, as well as the encoding can distinguish between bonds with the same bond length but of different types, which solves the problem that it is difficult to distinguish between these types of bonds with the traditional modeling method. The subsequent simulation results are basically consistent with the experimental graphical comparisons, providing a new modeling method and atomic encoding for the simulation modeling of etched structures and morphology prediction of other cut types.