Purple soils, developing from rapid physical weathering of nutrient rich sedimentary rock and classified as Inceptisols or Entisols in United States Department of Agriculture (USDA) Taxonomy, are the most important agricultural soils in the Sichuan basin of southwestern China. A portion of purple soils has been acidified and the acidification risk of these soils need further understanding. Here, electrodialysis (ED) was used to simulate the process of natural acidification of soils. We investigated the acidification risk of purple soils by ED treatments and compared its acidification characteristics with that of variable charge soils (Oxisol and Alfisol). Our results showed that the degree of acidification of purple soils after ED treatments was much higher than that of variable charge soils, although the purple soils contained more exchangeable base cations. There was no significant correlation between the purple soil acidity before and after ED treatments, however, the pH of purple soils after the ED treatments had a significant negative correlation (r = −0.680, P < 0.01) with the soil cation exchange capacity (CEC). We concluded that CEC (i.e., effective negative surface charges) played a decisive role in determining the acidification potential of purple soils. High content of clay minerals and low content of Fe/Al oxides in the purple soils lead to the higher amount of effective negative surface charge than that of variable charge soils, which induced the rise in the amount of H⁺ and Al³⁺ absorbed on the surface of purple soils and increased the acidification degree of purple soils remarkably. Therefore, compared to the variable charge soils, the purple soils had a higher acidification risk. These findings will provide a useful reference for the understanding of the acidification characteristics of purple soils.