© 2014, Springer-Verlag Berlin Heidelberg. Purpose: Soil acidification from chemical N fertilization has worsened and is a major yield-limiting factor in the red soil (Ferralic Cambisol) of southern China. Assessment of the acidification process under field conditions over a long term is essential to develop strategies for maintaining soil productivity. The objective of this study was to quantify soil acidification rates from chemical fertilizers and determine the amount of manure needed to inhibit the acidification process. Materials and methods: A long-term experiment with various fertilizations was carried out during 1990–2008 in a wheat–corn cropping system in the red soil of southern China. Treatments included non-fertilized control, chemical N only (N), chemical N and P (NP), chemical N, P and K (NPK), pig manure only (M), and NPK plus M (NPKM; 70 % total N from M). All N treatments had an input of 300 kg N ha−1 year−1. Annual soil sampling was carried out for pH measurement and acidity analysis. Results and discussion: Soil pH decreased sharply from an initial pH of 5.7 and then stabilized after 8 to 12 years of fertilization in the N, NP, and NPK treatments with a final pH of 4.2, 4.5, and 4.5, respectively. These three treatments significantly increased soil exchangeable acidity dominated by Al, decreased soil exchangeable base cations (Ca2+ and Mg2+), and elevated acidification rates (3.2–3.9 kmol H+ ha−1 year−1). In contrast, the manure applications (M or NPKM) showed either an increase or no change in soil pH and increases in soil exchangeable base cations. Conclusions: Urea application to the intensive cropping system accelerated acidification of the red soil during the 18-year field experiment. As 70 % or more total N source, continuous manure application can fully prevent or reverse red soil acidification process. As an effective animal waste management tool, manure incorporation into the acidic soil can promote the overall agricultural sustainability.