Conservation tillage and deep-side fertilization both hold the potential to reduce nitrogen leaching and improve grain yield and nitrogen use efficiency in fragrant rice cultivation practices. However, the combined impact of different tillage practices with deep-side fertilization on nitrogen leaching remains uncertain. Therefore, this study conducted on-site experiments for four rice-growing seasons in both early and late seasons in 2018 and 2019 using the fragrant rice varieties “Meixiangzhan 2” (MX) and “Xiangyaxiangzhan” (XY). The four experimental treatments included the following: conventional tillage with regular fertilization (T1), conventional tillage with simultaneous deep fertilization (T2), reduced tillage with simultaneous deep fertilization (T3), and no-tillage with simultaneous deep fertilization (T4). Our results indicate that the T4 treatment exhibited higher nitrogen leaching rates and potential nitrogen losses throughout the entire rice growth cycle, with a 4.51% increase in total mineral nitrogen leaching (TMNL) and a 1.86% increase in potential nitrogen leaching compared to T1 treatment. In contrast, the T2 treatment demonstrated the lowest nitrogen leaching rate, resulting in a 6.01% reduction in TMNL and a 9.57% decrease in potential nitrogen leaching compared to T1, demonstrating the most optimal performance. It is important to note that a reduction in nitrogen leaching does not directly translate into an increase in rice yield. Our study involved the cultivation of two fragrant rice varieties, ‘Meixiangzhan2’ (MX) and ‘Xiangyaxiangzhan’ (XY), and the results revealed some interesting insights. For MX, the T1 treatment resulted in lower daily grain outputs compared to the other treatments, with disparities ranging from 5.35% to 9.94%. Similarly, for XY, the T1 treatment yielded significantly lower daily grain outputs compared to the other treatments, with discrepancies ranging from 6.26% to 10.81% during the late season of 2019. Therefore, this study suggests that conventional tillage combined with deep fertilizer application can be considered as an effective agricultural strategy to reduce nitrogen leaching and enhance fragrant rice yields.