In order to clarify the reasonable application amount of nitrogen fertilizer in late japonica rice in the southern double season rice area, an field experiment was conducted in 2016—2017 during the late-rice cropping seasons in southern China, the six nitrogen levels including N1 (0 kg/hm²), N2 (165 kg/hm²), N3 (210 kg/hm²), N4 (255 kg/hm²), N5 (300 kg/hm²) and N6 (345 kg/hm²) were set, and the effects of different nitrogen application rates on the japonica rice yield, quality and nitrogen use efficiency were studied. The results showed that the yield of late japonica rice showed a parabolic trend with the increasing of nitrogen application. Compared with the yield of N4 plots, the grain yield of the N1, N2, N3, N5 and N6 plots decreased by 29.2%~34.9%, 10.1%~11.8%, 5.5%~5.7%, 1.2%~4.4% and 2.3%~9.0%, respectively. The grain yield of the N4 plots was significantly higher than those of the N1 and N2 plots in two years. The main reason for the increase of late japonica rice yield was the increase of productive panicle number and seed setting rate. With the increasing of nitrogen application, the total nitrogen accumulation of rice increased, while the nitrogen dry matter production efficiency, nitrogen physiological efficiency, nitrogen factor productivity for applied nitrogen, nitrogen agronomic efficiency and nitrogen harvest index were all decreased, and the nitrogen uptake and utilization efficiency first increased and then decreased. With the increasing of nitrogen application, the industrial quality, appearance quality and nutrition quality of the late japonica rice were all improved, the content of amylose content in eating and cooking quality decreased and the gel consistency increased. The peak viscosity, hot viscosity, cool viscosity and breakdown of RVA spectrum decreased gradually with the increasing of nitrogen application, while the setback and consistence increased. To sum up, it is advisable to apply nitrogen to N4 (255 kg/hm²) of japonica rice under the experimental conditions during the late-rice cropping seasons in southern China, which can reach the high yield, quality and efficiency.