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Fragrant rice has a high market value, and it is a popular rice type among consumers owing to its pleasant flavor. Plantation methods, nitrogen (N) fertilizers, and silicon (Si) fertilizers can affect the grain yield and fragrance of fragrant rice. However, the core commercial rice production attributes, namely the head rice yield (HRY) and 2-acetyl-1-pyrroline (2-AP) content of fragrant rice, under various nitrogen and silicon (N-Si) fertilization levels and different plantation methods remain unknown. The field experiment in this study was performed in the early seasons of 2018 and 2019 with two popular indica fragrant rice cultivars (Yuxiangyouzhan and Xiangyaxiangzhan). They were grown under six N-Si fertilization treatments (combinations of two levels of Si fertilizer, 0 kg Si ha−1 (Si0) and 150 kg Si ha−1 (Si1), and three levels of N fertilizer, 0 kg N ha−1 (N0), 150 kg N ha−1 (N1), and 220 kg N ha−1 (N2)) and three plantation methods (artificial transplanting (AT), mechanical transplanting (MT), and mechanical direct-seeding (MD)). The results showed that the N-Si fertilization treatments and all the plantation methods significantly affected the HRY and 2-AP content and related parameters of the two different fragrant rice cultivars. Compared with the Si0N0 treatment, the N-Si fertilization treatments resulted in higher HRY and 2-AP contents. The rates of brown rice, milled rice, head rice, and chalky rice of the fragrant rice also improved with the N-Si fertilization treatments. The N-Si fertilization treatments increased the activities of N metabolism enzymes and the accumulation of N and Si in various parts of the fragrant rice, and affected their antioxidant response parameters. The key parameters for the HRY and 2-AP content were assessed by redundancy analysis. Furthermore, the structural equation model revealed that the Si and N accumulation levels indirectly affected the HRY by affecting the N metabolism enzyme activity, N use efficiency, and grain quality of fragrant rice. Moreover, high N and Si accumulation directly promoted the 2-AP content or affected the antioxidant response parameters and indirectly regulated 2-AP synthesis. The interactions of the MT method with the N-Si fertilization treatments varied in the fragrant rice cultivars in terms of the HRY and 2-AP content, whereas the MD method was beneficial to the 2-AP content in both fragrant rice cultivars under the N-Si fertilization treatments.