Although cannabidiol and tetrahydrocannabinol in Cannabis species exert their pharmacological effects via the endocannabinoid system, it is believed that other phytochemicals, particularly terpenes, can modulate therapeutic outcomes through the entourage effect. Therefore, to gain a better understanding of the pharmacological effects of Cannabis, obtaining information on phytochemical compositions, including mono-, di-, and sesqui-terpenes in Cannabis species is essential. Applying a sophisticated analytical method is indispensable. In this study, headspace-gas chromatography/mass spectrometry (HS-GC/MS) was employed to identify major terpenes in the leaves and inflorescences of hybrid Cannabis species. The incubation time and temperature conditions for HS-GC/MS were optimized. This method was successfully applied to the leaves (n = 9) and inflorescences (n = 7) of hybrid Cannabis species. A total of 26 terpenes in Cannabis species were detected, and six major components, such as α-pinene (9.8-2270 μg/g), β-pinene (2.6-930 μg/g), myrcene (0.7-17,400 μg/g), limonene (1.3-300 μg/g), β-caryophyllene (60-3300 μg/g), and α-humulene (40-870 μg/g), were quantified. Each sample showed different terpene compositions, but six major terpenes among all the terpenes detected were consistently found in both the leaves and inflorescences of hybrid Cannabis species. In this study, the six major terpenes' potential in hybrid Cannabis species was evaluated as biomarkers to distinguish hybrid Cannabis species samples. This study contributes to a better understanding of the entourage effect of Cannabis-based botanical drugs.