Objective Panax notoginseng is an important Chinese medicinal plant. Saponin accumulation is higher in the flower buds than in the other parts of P. notoginseng. However, the flower bud compositions have not yet been quantified. The aim of this study is to investigate the formation and accumulation of saponins in the flower buds of P. notoginseng from different populations and at different growth years. Methods Fourteen types of P. notoginseng with different growing durations and from different areas of Wenshan County, Yunnan Province were collected. We separated P. notoginseng individually into the flower buds, stems, leaves, and roots at the places where it has the highest saponin content. An efficient high-performance liquid chromatography(HPLC) method was developed for simultaneously quantifying two active saponins, ginsenoside Rb1 and ginsenoside Rb3, in the flower buds of P. notoginseng. The total saponin content was determined by using a quantitative vanillin-sulfuric acid colorimetric method. HPLC method was used to establish the fingerprints of 13 saponins and then quantify the composition in the whole plant of P. notoginseng. Results The saponin contents of different parts differ significantly, and the total saponin content and those of Rb1 and Rb3 do not entirely correlated. The flower buds of P. notoginseng contain 27.79% of total saponins, which is the highest saponin content in the whole plant. Fingerprint result showed that different saponins were appeared in different parts of the plant, i.e. flower buds, stems, leaves, and roots.Conclusion The saponin contents from the flower buds of P. notoginseng vary depending on the growth area and duration. The fingerprints show that the saponin contents and compositions vary depending on the part of P. notoginseng. These results are useful for the pharmacological evaluation and quality control of P. notoginseng. Objective Panax notoginseng is an important Chinese medicinal plant. Saponin accumulation is higher in the flower buds than in the other parts of P. notoginseng. However, the flower bud compositions have not yet been quantified. The aim of this study is to investigate the formation and accumulation of saponins in the flower buds of P. notoginseng from different populations and at different growth years. Methods Fourteen types of P. notoginseng with different growing durations and from different areas of Wenshan County, Yunnan Province were collected. We separated P. notoginseng individually into the flower buds, stems, leaves, and roots at the places where it has the highest saponin content. An efficient high-performance liquid chromatography (HPLC) method was developed for simultaneously quantifying two active saponins, ginsenoside Rb1 and ginsenoside Rb3, in the flower safte of P. notoginseng. The total saponin content was determined by using a quantitative vanillin-sulfuric acid color imetric method. HPLC method was used to establish fingerprints of 13 saponins and then quantify the composition in the whole plant of P. notoginseng. Results The saponin contents of different parts differ significantly, and the total saponin content and those of Rb1 and Rb3 do not complete correlated. The flower buds of P. notoginseng contain 27.79% of total saponins, which is the highest saponin content in the whole plant. Fingerprint result showed that different saponins were appeared in different parts of the plant, ie flower buds, stems, leaves, and roots.Conclusion The saponin contents from the flower buds of P. notoginseng vary depending on the growth area and duration. The fingerprints show that the saponin contents and compositions vary based on the part of P. notoginseng. These results are useful for the pharmacological evaluation and quality control of P. notoginseng.