In the last 30 years, severe soil acidification has been found in China due to acid deposition and nitrogen fertilizer overuse. Understanding the spatial pattern and vertical variations in base saturation percentage (BSP) and exchangeable cations (Ca2+, Mg2+, K+, Na+, H+ and Al3+) can directly benefit fertilization management and ecological protection. Here, 1253 soil profiles were surveyed in tropical and subtropical regions in China to investigate the spatial variations in BSP and exchangeable cations at three soil depths of 0–20 cm, 20–50 cm and 50–100 cm. The spatial distributions were interpolated by using advanced machine learning techniques. We found that the exchangeable Ca2+ (Exch. Ca), Mg2+ (Exch. Mg) and BSP were significantly higher in paddy fields and uplands than in forests and gardens, regardless of soil depth, while the exchangeable K (Exch. K) did not significantly differ between various land-use types. The Exch. Ca and BSP in Anthrosols were significantly higher than those in Ferrosols, Argosols and Cambosols in the three soil layers. The spatial prediction results indicated that exchangeable cations and BSP were generally characterized by strong heterogeneity, and the Exch. Ca, Exch. K and exchangeable H+ (Exch. H) contents and BSP declined with increasing soil depth. This study helps us understand the spatial variation in BSP and exchangeable cations in the study area and benefits fertilization management and environmental protection.