The reserve of stem nonstructural carbohydrates (NSC) at heading can enhance the sink strength and improve the grain-filling ability of large-panicle rice, which is beneficial to realizing its high-yield potential. Delaying panicle nitrogen (N) application is expected to increase stem NSC accumulation, but the relevant technical parameters and their impact on the yield of large-panicle rice remain unclear. Two-year field experiments were conducted in 2021 and 2022 with two large-panicle rice cultivars (HLY280 and YLY228) and five panicle N treatments: panicle N application at emergence of 4th leaf from flag leaf (TL4), 3rd leaf from flag leaf (TL3), 2nd leaf from flag leaf (TL2), flag leaf (TL1), and no panicle N application (CK) as the control, to study the effect of different panicle N treatments on the accumulation and translocation of stem NSC, as well as their impact on rice yield and its components. The results showed that the panicle N treatments significantly influenced rice yield. Among the panicle N application treatments, TL3 showed the highest yield for both cultivars over two years. Compared with TL4, TL3 significantly increased the percentage of filled grains and grain weight while maintaining a similar number of spikelets per panicle, which increased the yield of HLY280 and YLY228 by 10.1–13.6% and 12.4–12.7%, respectively. Among the panicle N application treatments, TL3 significantly increased the translocation of stem mass (net output of stem mass) and stem NSC (∆NSC) from heading to 15 days after heading (DAH), which led to the highest dry matter accumulation during the initiation of grain filling from heading to 15 DAH. The higher ∆NSC of TL3 was mainly due to the higher stem NSC at heading, which was contributed by the higher stem NSC accumulation from 5 days before heading (DBH) to heading. Additionally, the higher stem NSC accumulation under TL3 from 5 DBH to heading was significantly positively correlated with the higher leaf area duration (LAD) in this period. These results suggest that delaying panicle N application to TL3 can significantly increase the yield of large-panicle rice compared with TL4 by increasing the percentage of filled grains and grain weight, which is the result of increased stem NSC accumulation.