A long-term stationary field experiment consisting of 5 fertilization treatments was carried out in the Red Soil Ecological Experiment Station of CAS to study effects of fertilization on pH and exchangeable H+ and Al3+ in soil and analyze relationships of organic matter (OM) content with soil pH, and contents of exchangeable H+ and Al3+. Results show that fertilization in all treatments increased soil pH and decreased contents of exchangeable H+ and Al3+. Treatment M (organic manure), Treatment BM (organic manure + microbial agent) and Treatment BMT (organic manure + microbial agent + microelement fertilizer ) were significantly superior to Treatment F (chemical fertilizer) and Treatment TF (chemical fertilizer + microelement fertilizer) in reducing soil acidity. Addition of microelements and microbial agent increased the contents of exchangeable H+ and Al3+ slightly. Soil OM content was significantly correlated positively with soil pH value, and negatively with exchangeable Al3+ content, but not significantly related with exchangeable H+ content. With rising soil OM content, the proportion of exchangeable H+ increased in exchangeable acidity of soil. Long-term application of organic manure to increase soil OM content is a good agronomic practice to reduce acidity and aluminum toxicity in red soil.