Hedychium spicatum Sm. is an endangered herb which grows preferably in humid tropics and subtropics known for its distinct camphoraceous flavour and medicinal properties. The essential oils of H. spicatum rhizomes from six different natural habitats at different altitudes in Uttarakhand, India were analyzed. Twenty compounds were identified, accounting for 87.4–98.5% of the essential oils, with 1,8-cineole (33.4–41.9%), α-terpinene (39.6%), camphor (31.4%), and linalool (29.9%), being the prevalent major constituents of all accessions. HS-ALM (H. spicatum rhizomes Almora essential oil), HS-DDN (H. spicatum rhizomes Dehradun essential oil), HS-PAU (H. spicatum rhizomes Pauri essential oil), HS-TEH (H. spicatum rhizomes Tehri essential oil), and HS-USN (H. spicatum rhizomes Udham Singh Nagar essential oil) were dominated by oxygenated monoterpenes with 43.1–74.0%, respectively. In contrast, in HS-PIT (H. spicatum rhizomes Pithoragarh essential oil), hydrogenated monoterpenes dominated 57.8% of the total oil constituents. All accessions were assessed for significant nematicidal potential against Meloidogyne incognita and insecticidal potential against Spodoptera litura. The proteins/enzymes used for validation using docking studies were acetylcholinesterase (PBD ID: IC2O) and carboxylesterase (PDB ID: 1CI8). The study produced significant outcomes, showing the binding energy estimation of tested oil components to active sites supported the structure-activity relationship with bioinformatics tools.