Increasing acid deposition and intense nitrogen (N) fertilization have resulted in severe soil acidification in many regions of the world. However, the soil acidification rate, especially quantitative contributions of different proton (H⁺) sources remain unclear in various cropping systems. In this study, a two-year field lysimeter experiment was conducted with a set of different N fertilization treatments (0, 100, 200 and 400 kg N ha⁻¹ yr⁻¹) for maize crop in typical red soil in subtropical China. The pathways and budgets of different H⁺ sources were quantified by calculating the input–output balance of major elements. Results showed that fertilization significantly accelerated soil acidification by increasing the leaching of NO₃^– and base cations (K⁺, Ca²⁺, Na⁺, and Mg²⁺) as well as increasing the cation removals by plant uptake and harvest. Unbalanced plant uptake of anions and cations was the primary H⁺ source (64.4–80.5%) to soils. Plants have an important effect on soil acidification by redistributing cations in soils. Due to cation removals by plant uptake and harvest, there were significant decreases of soil exchangeable base cations under high urea-N treatments (200 and 400 kg N ha⁻¹ yr⁻¹) and significant increases of soil exchangeable H⁺ and Al³⁺ under three fertilization treatments. Of course, N transformation also plays an important role (12.1% to 38.8%). However, the effect of direct H⁺ deposition is minor in this area comparatively (5.78% to 7.34%). Quantification of acidification contribution of different sources is useful for the establishment of further soil remediation practices. The field management is considered very important to alleviate soil acidification, including increasing straw return and controlling fertilizer application.