Panax notoginseng is a medicinal plant in China, the flowers of which have high medicinal value. To study the differences in the floral fragrance compounds of P. notoginseng flowers (bionic wild cultivation) from the forests of Yunnan Province, the floral fragrance compounds from four varieties of P. notoginseng flowers (four-forked seven leaves, three-forked seven leaves, four-forked five–seven leaves, and three-forked five–six leaves) were compared and analyzed via headspace solid phase microextraction combined with gas chromatography–mass spectrometry methods. A total of 53 floral fragrance compounds from the P. notoginseng flowers were divided into eight categories, mainly consisting of terpenes, alkynes, aromatic hydrocarbons, and alcohols. Moreover, high contents of 3-carene, germacrene D, (−)-α-gurjunene, valencene, (+)-γ-gurjunene, menogene, and aromandendrene were identified from the flowers of different P. notoginseng varieties. Interestingly, floral fragrance compounds such as 3-carene, valencene, aromandendrene, menogene, and (+)-γ-gurjunene were first reported in the flowers of P. notoginseng. Cluster analysis showed that P. notoginseng with four-forked and three-forked leaves clustered into two subgroups, respectively. In addition, principal component analysis showed that (+)-γ-gurjunene, (+)-calarene, copaene, 1,8,12-bisabolatriene, γ-elemene, (–)-aristolene, caryophyllene, 3-carenes, and 2,6-dimethyl-1,3,6-heptatriene can be used to distinguish the floral fragrance components of four P. notoginseng flower species. This study provides a theoretical basis for elucidating the floral fragrance compounds emitted from the flowers of different P. notoginseng varieties in an agroforestry system.