An innovative, integrated strategy was developed for rapid and comprehensive quality assessment of Ligusticum chuanxiong Hort., the key raw material for Guanxinning tablets. This approach simultaneously evaluates both chemical composition and biological activity. Initially, an HPLC method was developed for the determination of the content of five bioactive compounds, including ferulic acid, senkyunolide I, senkyunolide H, senkyunolide A and ligustilide. Moisture content was also measured with a rapid moisture analyzer. Meanwhile, hyperspectral images of different batches of the herb in the range of 380-1064 nm was collected. Furthermore, anti-thrombotic activity of the herb was rapidly evaluated using a zebrafish thrombosis model. Finally, quantitative calibration models were established using both partial least squares regression and advanced DenseNet121 algorithms. The DenseNet121 model demonstrated exceptional performance, achieving R2p values of 0.9812, 0.9669, 0.9945, 0.9942, 0.9900, 0.9814, and 0.9892 for the evaluated quality parameters. This strategy was successfully applied to evaluate 201 batches of Ligusticum chuanxiong Hort., with quality variations visualized through a Shewhart control chart. The developed approach represents a robust, efficient, and precise method for holistic quality evaluation of Guanxinning tablet raw materials, offering significant advantages for pharmaceutical quality control.