Agricultural soil acidification in China is known to be caused by the over-application of nitrogen (N) fertilizers, but the long-term impacts of different fertilization practices on intensive cropland soil acidification are largely unknown. Here, we further developed the soil acidification model VSD+ for intensive agricultural systems and validated it against observed data from three long-term fertilization experiments in China. The model simulated well the changes in soil pH and base saturation over the last 20 years. The validated model was adopted to quantify the contribution of N and base cation (BC) fluxes to soil acidification. The net NO3- leaching and NO4+input accounted for 80% of the proton production under N application, whereas one-third of acid was produced by BC uptake when N was not applied. The simulated long-term (1990-2050) effects of different fertilizations on soil acidification showed that balanced N application combined with manure application avoids reduction of both soil pH and base saturation, while application of calcium nitrate and liming increases these two soil properties. Reducing NH4+ input and NO3- leaching by optimizing N management and increasing BC inputs by manure application thus already seem to be effective approaches to mitigating soil acidification in intensive cropland systems.