Nanogrooves with high aspect ratios possess small size effects and high-precision optical control capabilities, as well as high specific surface area and catalytic performance, demonstrating significant application value in the fields of optics, semiconductor processes, and biosensing. However, existing manufacturing methods face issues such as complexity, high costs, low efficiency, and low precision, especially in the difficulty of fabricating nanogrooves with high resolution on the nanoscale. This study proposes a method based on focused ion beam technology and a layer-by-layer etching process, successfully preparing V-shaped and rectangular nanogrooves on a silicon dioxide substrate. Combining with cellular automaton algorithm, the ion sputtering flux and redeposition model was simulated. By converting three-dimensional grooves to discrete rectangular slices through a continuous etching process and utilizing the sputtering and redeposition effects of gallium ion beams, high-aspect-ratio V-shaped grooves with up to 9.6:1 and rectangular grooves with nearly vertical sidewalls were achieved. In addition, the morphology and composition of the V-shaped groove sidewall were analyzed in detail using transmission electron microscopy (TEM) and tomography techniques. The influence of the etching process parameters (ion current, dwell time, scan times, and pixel overlap ratio) on groove size was analyzed, and the optimized process parameters were obtained.