To elucidate the driving mechanisms of different fertilization practices on soil acidification, a case study was conducted using double-cropping rice fields and pomelo orchards as experimental systems. The effects of conventional nitrogen and phosphorus fertilizers, along with their co-application with organic fertilizers, on acidification rates were examined. Results demonstrated that in double-cropping rice fields, acidification rates were 24.55, 7.42, 4.32, and -0.81 keq/hm2/yr, respectively when applying ammonium sulfate + calcium-magnesium phosphate, urea + superphosphate, urea + calcium-magnesium phosphate, and urea + calcium-magnesium phosphate with 20% chemical nitrogen replaced by organic fertilizer. In pomelo orchards, acidification rates were16.96 keq/hm2/yr (ammonium sulfate + calcium-magnesium phosphate), 9.09 keq/hm2/yr (urea + superphosphate), and 6.48 keq/hm2/yr (urea + calcium-magnesium phosphate) when combining 20% chemical fertilizer substitution with organic fertilizer, whereas it was 0.51 keq/hm2/yr in treatment with urea + organic fertilizer with 40% chemical nitrogen and total phosphorus replacement, +, 20% nitrogen reduction The nitrogen transformation processes associated with ammonium sulfate application, nutrient uptake by plants, and the acidity of superphosphate constitute were major sources of protons contributing to soil acidification. Conversely, alkaline substances in organic fertilizer or calcium-magnesium phosphate could consume significant protons. In paddy fields, alkaline water irrigation and nitrogen transformation processes driven by organic nitrogen fertilizer were important proton consumption processes. Therefore, the optimal fertilization mitigations strategies are: for paddy fields, replacement of 20% chemical nitrogen with organic fertilizer combined with urea and calcium-magnesium phosphate; for pomelo orchards, replacement of 40% chemical nitrogen and all phosphate fertilizer with urea and organic fertilizer alongside 20% nitrogen reduction.