Two japonica rice cultivars with different panicle trait index (PTI), HP917 (a high-PTI cultivar) and DP128 (a low-PTI cultivar) were used to investigate the effects of the nitrogen (N) rate and plant density on the grain distribution of secondary branches on the panicle axis, leaf photosynthetic characteristics, and grain yield by a split plot design. The main plots were assigned to four N rates (0, 140, 200, and 260 kg ha), and the subplots were assigned to two plant densities: (D, 15 plants m; D, 30 plants m). Results showed that the grain yield was increased by increasing N rate and plant density, reaching a peak at N with D. Compared with N treatment, the PTIs of HP917 and DP128 increased with an increase in the N rate, respectively. The PTIs of HP917 and DP128 increased by 4% with increasing plant density from D to D. The leaf capacity was significantly affected by N rate and plant density. The grain distribution characteristics of secondary branches on the panicle axis was closely related to yield. Correlation analysis showed the PTI was positively correlated with grain yield and net photosynthetic rate. These results suggested the improvement in PTI from 0.15 to 0.52 was beneficial to increase the grain yield, which might contribute to the increased grain number of secondary branches of the middle and bottom panicle.