A field experiment was conducted to study rice yields, characteristics of N use efficiency and soil nutrients under controlled-release fertilizers (as urea formaldehyde-based one (NC) and lignin-based one (MC)) as basal fertilizer and ammonium urea as topdressing, which were contrasted by traditional formula fertilizer as basal fertilizer and urea as two topdressing (abbreviated as CG). The results showed that the treatments of controlled-release fertilizers as basal fertilizer and ammonium urea as tillering topdressing had no significant effect on rice yield compared to CG. However, compared to CG, NC and MC with basal fertilizers and ammonium urea as panicle fertilizer (abbreviated as NC-S and MC-S, respectively) significantly increased yield by 3.96% and 6.01%, respectively, which should be attributed to 16.7% and 17.6% respectively higher than CG in spikelet number per panicle, meanwhile, they significantly increased nitrogen accumulation in above-ground parts of rice by 10.0% and 11.6%. Compared to CG, NC and MC as basal fertilizers and ammonium urea as tillering fertilizer (abbreviated as NC-F and MC-F, respectively) increased nitngen accumulation by 2.50% and 5.89%, respectively, meanwhile, they increased nitrogen use efficiencies (NUE) by 3.96% and 6.01%, respectively. The treatments of controlled-release fertilizers as basal fertilizer and urea ammonium as topdressing enhanced both nitrogen uptake efficiency (NupE) and apparent nitngen apparent recovery (ANR), of which MC-S significantly increased NupE by 11.6% than CG, NC-S and MC-S significantly increased ANR by 25.4% and 29.3% than CG, respectively. The treatments of controlled-release fertilizers as basal fertilizer and ammonium urea as topdressing significantly enhanced soil alkali hydrolyzable nitvogen by 6.58%-10.7% compared to CG, of which the treatments with ammonium urea as panicle fertilizer showed better effect, meanwhile, organic matter contents were found 1.11%-7.56% higher than CG. Therefore, controlled-release fertilizers as basal fertilizer and ammonium urea as panicle fertilizer is more conducive to improve rice yield and characteristics of nitrogen use efficiency, and increase soil fertility.