The deep application of fertilizers 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, deep application of fertilizers, reduced application of nitrogen fertilizers, and combination with nitrification inhibitors or lime on maize growth and nutrients in acidic soil. The results showed that compared with surface application of fertilizers, deep application of fertilizers 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 deep fertilization did not significantly affect maize biomass, root architecture, and nitrogen and phosphorus uptake. Deep application of fertilizers mainly increased root biomass, root length, root surface area, and nitrogen uptake in the 0-8 cm and 8-16 cm soil layers, as well as increased available and total phosphorus content in the 8-16 cm soil layer and ammonium nitrogen content in the 8-16 cm and 16-24 cm soil layers. Therefore, deep fertilization measure in acidic soils should be more effective in improving crop growth and nitrogen fertilizer utilization than lime and nitrification inhibitors, showing good application prospects.