【Objective】The combined application of biological nitrification inhibitors (BNIs) with chemical nitrogen (N) fertilizers reduces N loss and enhances nitrogen use efficiency (NUE). However, research on their combined use with organic N fertilizers remains limited, and their yield-enhancing effects and underlying mechanisms remain unclear. 【Method】This study employed organic Chrysanthemum morifolium Ramat cv. ‘Hangbaiju’ in field trials, establishing four treatments: no nitrogen application (-N), fish protein organic water-soluble fertilizer (N), N+50 g·kg-1 methyl 3-(4-hydroxyphenyl) propionate (MHPP), and N+50 g·kg-1 salicylic acid (SA). The research investigated the effects of combining BNIs with organic N fertilizers on chrysanthemum yield, quality, and the underlying synergistic mechanisms. 【Result】 Results indicated that the N+SA treatment yielded the highest harvest at 6 154 kg·hm-2, achieving a 40.2% increase in yield (P < 0.05), a 9.1% rise in total flavonoids (P < 0.05), and a 75.0% improvement in NUE (P < 0.05) compared to the N treatment. Compared with the N treatment, N+MHPP showed a trend of increasing yield and enhancing NUE. N+SA significantly increased total root length by 147.7% and fresh root biomass by 127%, with root-promoting effects significantly superior to N+MHPP. Principal component analysis indicated positive correlations between Chrysanthemum morifolium Ramat cv. ‘Hangbaiju’ yield and NUE with root length, root surface area, and root volume. It is speculated that the application of SA may achieve synergistic effects of “increased yield, enhanced efficiency, and improved quality” by optimizing the root architecture of Chrysanthemum morifolium Ramat cv. ‘Hangbaiju’, enhancing nitrogen uptake, and potentially exhibiting growth-promoting activity.【Conclusion】This study confirms the significant potential of BNIs in boosting yield, efficiency, and quality within organic water-soluble fertilizer systems, providing a new pathway for green and efficient fertilization of organic medicinal crops.