The deep application of fertilizers (DF) effectively improves soil nutrient utilization and crop yield, but there is little research on the application effect in acidic soils. This study compared the effects of surface application of fertilizers (SF), DF, reduced application of nitrogen fertilizers (RN) and combination with nitrification inhibitors or lime on maize growth and nutrient uptake in acidic soil. The results showed that compared with SF, DF significantly increased maize biomass, root length, root surface area, root volume, and underground nitrogen absorption. The application of lime or nitrification inhibitors in combination with DF did not significantly affect maize biomass, root architecture, and nitrogen and phosphorus uptake. DF mainly increased root biomass, root lengths, root surface areas, and nitrogen uptake in the 0-8 cm and 8-16 cm soil layers, as well as increased available phosphorus content in the 8-16 cm soil layer and ammonium nitrogen contents in the 8-16 cm and 16-24 cm soil layers. Therefore, DF in acidic soils is likely more effective in improving crop growth and nitrogen fertilizer utilization, showing good application prospects.