Juvenile hormone compounds belong to a family of acyclic sesquiterpenoids, biosynthesized within small paired endocrine glands of corpora allata-corpora cardiaca having a neural connection with the brain. Stringent regulation of JH-levels in insect haemolymph is one of the most critical factors ensuring normal growth and development in insects. JHAMT is characterized as a key regulatory enzyme playing a pivotal role during insect metamorphosis and reproduction physiology by catalyzing the final step of SAM-dependent methylation of JH-acids into their cognate methyl esters. Recent reports on biochemical and molecular characterization of JHAMT gene from different insect species have proposed the JHAMT enzymatic activity as a potential target for the development of novel small molecule insect growth regulator(s). Therefore, in the present study, the protein sequence identity dependent homology model for JHAMT protein from a polyphagous pest, Helicoverpa armigera (order: Lepidoptera) has been generated and subsequently explored for virtual screening against small molecules natural product library. One such promising compouns namely, Scolimoside (HMDB05799) showing interactions with amino acid residues of enzyme's substrate-binding pocket (SBP) was further validated using molecular docking and Molecular Dynamics simulation (MD simulation). The study may pave the way forward for the design and development of novel eco-friendly small regulatory molecules as a component of integrated pest management.