This study provides an important basis for the directional breeding of P. notoginseng cultivars: P. notoginseng “Zijing” is suitable for development into medicinal materials enriched in Rb1/Rd and applicable to the production of drugs for treating cardiovascular and cerebrovascular diseases; P. notoginseng “Dianqi No.1” can serve as a cultivar for the specific extraction of Re to meet the demand for neuroprotective drugs; the stability of Rg1 suggests that it can be used as a reference index for evaluating the quality consistency of P. notoginseng, thereby reducing batch-to-batch differences. This evidence concerns the gene PPP1R3A and cerebrovascular disorder.