Yield loss of the ratoon crop due to rolling damage during the mechanical harvesting of the main crop (MEC) severely limits the promotion of mechanized rice ratooning technology. Our previous study showed that MEC changed the population structure of the ratoon crop by forming a rolled zone and non‐rolled zone (NRZ), resulting in a positive border effect on the yield of the NRZ, which reduced the yield loss. Nitrogen (N) management has a great impact on matter accumulation and yield formation in ratoon crops. However, it remains unclear whether the border effect on the yield of NRZ is affected by the N rate. The hypothesis is that N rates would affect the border effect on NRZ yield, thereby increasing or decreasing yield loss. To address this question, field experiments were conducted with two harvest methods for the main crop (MEC: mechanical harvesting, MAN: manual harvesting) and three N rates for the ratoon crop (N0: 0, MN: 120, and HN: 180 kg N ha−1) in 2021 and 2022. The results showed that the yield loss declined from 22.4% to 13.2% as the N rate increased from 0 to 180 kg ha−1. The reduction in yield loss was attributed to the increased border effect of higher N supply on NRZ yield. The border effect on NRZ yield was −7.0%, 5.0%, and 10.7% in N0, MN, and HN, respectively. Compared with MAN, the yield reduction of NRZ in N0 was mainly due to the lower yield of the nonrolled side row (R2) and middle row (R3), while the yield increase in NRZ in MN was mainly due to the increased yield of the nonrolled single row (R1), and the yield increase in NRZ in HN was mainly due to the increased yield of both R1 and R2. A high N rate improved root vigor and increased the N uptake and leaf area index of nonrolled rows in MEC, which increased the panicles m−2 and total dry matter weight. With the increase in the N rate, the border effect on these yield attributes of R1 and R2 gradually increased, especially for R1, thereby increasing the border effect on the NRZ yield. Our results indicate that the border effect on the NRZ yield was affected by the N rate. High N supply reduced yield loss of the ratoon crop by increasing the border effect on NRZ yield. The appropriate N rate should be further determined to balance the yield and economic and environmental benefits of the ratoon crop in mechanized rice ratooning systems.