Addressing the limitation that existing soil acidification studies are mostly confined to the surface layer, lacking vertical spatial differentiation characterization and supporting evidence for deep-layer management, this study aims to quantify the vertical characteristics and spatial differentiation pattern of soil acidification in Sichuan Province during 1980s–2010s, and propose scientific and rational regional differentiated prevention and control strategies based on the Depth Index (DI). Based on soil pH depth raster data from two periods in Sichuan Province, this study utilized the depth-weighted average method to reconstruct the standard topsoil (0–20 cm) and subsoil (20–40 cm) layers. The DI was constructed to quantify the relative intensity of acidification between the topsoil and subsoil. Finally, regional prevention and control analysis was conducted by combining the spatial distribution map of DI across six major regions. The study reveals that soil acidification in Sichuan Province is generally dominated by topsoil acidification. The DI distribution indicates significant vertical spatial differentiation among regions: areas dominated by topsoil acidification, such as the Chengdu Plain region, account for 76.21% of the total area, while the mountainous region of Southwestern Sichuan exhibits a subsoil-dominated pattern, with topsoil acidification area accounting for only 38.52%.Vertical acidification management must be implemented regionally and differentially. Considering regional ecological environments, measures such as shallow layer amelioration combined with the application of alkaline parent rock fragments are recommended for areas strongly dominated by topsoil acidification. For subsoil-dominated areas, the depth of acidification remediation measures must be increased, and further investigation into the mechanism of deep-layer acidification should be carried out to achieve precise policy implementation.