The application of panicle nitrogen fertilizer is an important management measure to increase rice yield, but its effect and mechanism of application rates on the yield increase of super rice varieties with different panicle sizes are still unclear. In this study, three super rice varieties with large differences in panicle sizes (indicated by the spikelet number per panicle) of Nanjing 9108 (small panicle size), Yangliangyou 6 (medium panicle size), and Yongyou 1540 (large panicle size) were selected as materials. Under the condition of the same amount of base-tiller fertilizer (162 kg N hm-2), the effects of five panicle nitrogen fertilizer rates (PNR) of 0, 54, 108, 162, and 216 kg hm-2 on the yield of the above rice varieties were studied. And its regulatory effects on the differentiation and degeneration of spikelets and related morphophysiological indices after heading were observed. The results were as follows: (1) In the PNR range of 0-216 kg hm-2, the spikelet number per panicle gradually increased but the seed-setting rate and 1000-grain weight gradually decreased with the increase of PNR. And the higher the PNR, the more obvious the decrease of seed-setting rate and 1000-grain weight. Three rice varieties, Nanjing 9108, Yangliangyou 6, and Yongyou 1540, had the highest yields in the PNR of 162-216, 108-162, and 54-108 kg hm-2, respectively. According to the curve equation of grain yield and PNR, the optimal PNR for high yields of the above three varieties were calculated to be 177.6-182.0, 134.3-136.3, and 109.9-125.7 kg hm-2, respectively. (2) In general, rice varieties with large panicle sizes had higher yields, while rice varieties with small panicle sizes had greater yield-increasing effects of PNR. The number of differentiated and surviving secondary spikelets in rice varieties with small panicle size increased greatly after application of panicle nitrogen fertilizer, which was the main reason that the yield-increasing effect was higher than that of rice varieties with medium and large panicle size. (3) Under the condition of high-yield PNR, high effective leaf area ratio, grain-leaf ratio (spikelet/leaf area, filled grain/leaf area, and grain weight/leaf area), non-structural carbohydrate (NSC) translocation amount, sugar-spikelet ratio, root oxidation activity, activity root of spikelet and zeatin (Z) + zeatin riboside (ZR) content in grains and roots from 0-40 day(s) after heading of three rice varieties were high. Correlation analysis showed that the yields of super rice varieties with different panicle sizes and the above indicators basically had a significant or extremely significant positive correlation. These results indicated that the PNR should be adjusted according to the panicle size. The appropriate PNR was beneficial to maintain a high effective leaf area ratio, grain-leaf ratio, NSC translocation amount, sugar-spikelet ratio, root oxidation activity, activity root of spikelet, and Z + ZR content in grains and roots after heading under the premise of higher total spikelets. This helped to maintain a high seed-setting rate and grain weight, thereby ultimately increasing the grain yield.