Objective To address the problems of rhizospheric microenvironment deterioration and medicinal quality decline caused by continuous cropping obstacles of Fritillaria unibracteata Hsiao et K. C. Hsia, this study explored the regulatory effects of different concentrations of salicylic acid (SA) under continuous and non-continuous cropping patterns and clarified the optimal SA concentration and underlying mechanism for alleviating continuous cropping obstacles, aiming to provide a theoretical basis for optimizing cultivation techniques. Methods A pot experiment was conducted with two cultivation patterns (continuous cropping and non-continuous cropping) and six SA concentration gradients (0, 20, 50, 100, 200, and 500 μmol/L). The changes in root exudates, soil physicochemical properties, soil enzyme activities, alkaloid content, and microbial community structure were determined. Correlation analysis and redundancy analysis (RDA) were performed to elucidate the regulation mechanism. Results SA exerted significant concentration-specific regulatory effects on the rhizospheric microenvironment and alkaloid biosynthesis of F. unibracteata, showcasing a significant interaction effect with cultivation patterns. Total phenolic acids in root exudates increased under 20 μmol/L and 500 μmol/L SA treatments (P<0.05), and organic acids reached the peak under 200 μmol/L SA treatment. The soil organic carbon and soil organic matter in the non-continuous cropping group were significantly higher than those in the continuous cropping group. SA at 50 μmol/L optimized soil pH, increased the supply of available phosphorus and ammonium nitrogen, and enhanced the activities of urease and acid phosphatase. Pseudomonadota and Ascomycota were the dominant phyla in bacterial and fungal communities, respectively. SA at 500 μmol/L enriched beneficial microorganisms such as Streptomyces, inhibited pathogens, and specifically increased the content of peimisine and sipeimine. RDA results showed that SA remodeled the microbial community by regulating the composition of root exudates, thereby mediating alkaloid biosynthesis. Conclusion SA at 50 μmol/L SA is suitable for optimizing rhizosphere nutrient supply and enzyme activities, and that at 500 μmol/L is suitable for effectively alleviating continuous cropping obstacles and promoting the accumulation of medicinal alkaloids. SA achieves rhizospheric ecological restoration and medicinal quality improvement through a synergistic pathway of regulating root exudate composition, remodeling microbial community structure, and repairing rhizospheric interaction network. This study provides a new approach for the management of continuous cropping obstacles for F. unibracteata.