Subsoil acidity seriously inhibits the development of agriculture and forestry in southern China. However, there are few effective methods for amelioration of subsoil acidity. In order to develop low cost and efficient methods for amelioration of subsoil acidity through surface application of amendments, a column leaching experiment and an in situ field experiment were conducted to investigate the amelioration effects of surface application of alkaline slag (AS) and phosphogypsum (PG) on the soil properties in an Ultisol profile. AS increased soil pH and base saturation, and decreased exchangeable acidity of the different segments in the soil profile to different degrees. Since AS contains a high content of soluble chloride, the quick leaching of chloride ions promoted the migration of base cations in the amendments through the soil profile, the exchange of base cations with exchangeable aluminum (Al) and manganese (Mn), and the leaching of soluble Al and Mn out of the profile. Although PG could increase the soil exchangeable calcium (Ca), PG significantly increased the soluble Al and Mn in the Ultisol profile. Compared with PG, AS was more effective in decreasing soil acidity and soluble Al and Mn, and increasing exchangeable Ca and magnesium (Mg) in the Ultisol profile. Therefore, AS was superior to PG in ameliorating soil acidity in the surface soil and subsoil of this Ultisol.