The invention provides a panax notoginseng saponin composition and a preparation method and application thereof.The composition is prepared from, by weight, 30-50% of ginsenoside Rg1, 25-40% of ginsenoside Rb1, 7-16% of notoginsenoside R1, 2.7-8% of ginsenoside Re, 0.5-7.0% of ginsenoside Rd, 0.5-2% of ginsenoside Rf, 0.3-2.0% of ginsenoside Rh2, 1-3% of ginsenoside Rc, 0.3-2.5% of ginsenoside Rb3 and 0.5-2.5% of ginsenoside Rg3, wherein ginsenoside Rg1, ginsenoside Rb1 and notoginsenoside R1 account for 70-95% of the total weight of the active components, and the sum of the contents of ginsenoside Rb1 and notoginsenoside R1 is not smaller than 8 times of the content of ginsenoside Rd.Compared with commercially available Xueshuantong injections and Xueshuantong preparations, the panax notoginseng saponin composition has a more obvious arterial and venous thrombosis resistant effect, low toxicity and high safety.