Long-term fertilization experiment provides the platform for understanding the proton budgets in nitrogen transformations of agricultural ecosystems.We analyzed the historical(1990-2005) observations on four agricultural long-term experiments in China(Changping,Chongqing,Gongzhuling and Qiyang) under four different fertilizations,i.e.,no-fertilizer(control),sole chemical nitrogen fertilizer(F N),sole chemical phosphorous and potassium fertilizers(F PK) and chemical nitrogen,phosphorous and potassium fertilizers(F NPK).The significant decline in topsoil pH was caused not only by chemical N fertilization(0.29 and 0.89 pH at Gongzhuling and Qiyang,respectively) but also by chemical PK fertilization(0.59 pH at Gongzhuling).The enhancement of available nutrients in the topsoil due to long-term direct nutrients supply with chemical fertilizers was in the descending order of available P(168-599%)>available K(16-189%)>available N(9-33%).The relative rate of soil pH decline was lower under long-term judicious chemical fertilization(-0.036-0.034 pH yr-1) than that under long-term sole N or PK fertilization(0.016-0.086 pH yr-1).Long-term judicious chemical fertilization with N,P and K elements decreases the nutritional limitation to normal crop growth,under which more N output was distributed in biomass removal rather than the loss via nitrate leaching.We concluded that the N distribution percentage of nitrate leaching to biomass removal might be a suitable indicator to the sensitivity of agricultural ecosystems to acid inputs. Long-term fertilization experiment provides the platform for understanding the proton budgets in nitrogen transformations of agricultural ecosystems.We analyzed the historical (1990-2005) observations on four agricultural long-term experiments in China (Changping, Chongqing, Gongzhuling and Qiyang) under four different fertilizations, ie, no-fertilizer (control), sole chemical nitrogen fertilizer (FN), sole chemical phosphorous and potassium fertilizers (F PK) and chemical nitrogen, phosphorous and potassium fertilizers caused not only by chemical N fertilization (0.29 and 0.89 pH at Gongzhuling and Qiyang, respectively) but also by chemical PK fertilization (0.59 pH at Gongzhuling). The enhancement of available nutrients in the topsoil due to long-term direct nutrients supply with chemical Fertilizers was in the descending order of available P (168-599%)> available K (16-189%)> available N (9-33%). The relative rate of soil pH decline was lower under long -term judicious chemical fertilization (-0.036-0.034 pH yr-1) than that under long-term sole N or PK fertilization (0.016-0.086 pH yr-1) .Long-term judicious chemical fertilization with N, P and K decreases. the nutritional limit to normal crop growth, under which more N output was distributed in biomass removal rather than the loss via nitrate leaching. We concluded that the N distribution percentage of nitrate leaching to biomass removal might be a suitable indicator to the sensitivity of agricultural ecosystems to acid inputs.