We investigated whether the one-time application of polymer-coated urea (PCU) before transplanting could simultaneously improve the grain yield and nitrogen use efficiency (NUE) of japonica-indica hybrid rice (JIHR) through a field experiment. The local high-yield JIHR cultivar Chunyou-927 was field grown during the rice-growing seasons in 2019 and 2020. The experiment consisted of three treatments: no nitrogen application (0N), application of conventional urea (CU), and the one-time application of PCU. Grain yield was 1.0–1.3 t/ha higher, and agronomic NUE (kg grain yield increase per kg N applied) was 5.2–5.9 kg/kg higher, respectively, under the PCU treatment compared with the CU treatment across the two study years. When compared with the CU treatment, the PCU treatment could (1) improve root morphological trait, (2) reduce redundant vegetative growth during the early growth period, (3) increase matter production during the mid and late growth period, and (4) increase plant activity during the grain-filling period. Overall, our findings indicate that one-time PCU application before transplanting of the JIHR cultivar holds great promise for increasing grain yield and NUE.