Panax notoginseng is often used to promote blood circulation for the intervention of cardiovascular diseases (CVDs), while the flower of Panax notoginseng (PF) is used in folk remedies for the amelioration of hypertension in the Yunnan Province of China as a tea and is increasing in popularity throughout Asia. Previous studies on the Panax notoginseng were mainly focused on the root such that limited research on the flower cannot feed the need of increasing consumption and the products quality and pharmacological profile remains to be well characterized. In this study, chromatographic fingerprints and angiogenesis activities of different batches of commercial PF decoction were determined and then multiple regression analysis was performed to analyze their spectrum-effect relationships. The results of chromatographic fingerprints and zebrafish angiogenesis bioassay indicated the significant heterogeneities in the twelve batches of commercial PF products. Multiple regression analysis on the spectrums-activities relationship provided clues on the bioactive chemical markers of PF that may be developed as quality standards of PF.