Experimental techniques, such as vibrational spectroscopy (FT-IR and FT-Raman), UV-visible, thermal analysis (DSC), along with quantum chemical calculations based on density functional theory (DFT) were conducted to explore the physicochemical properties of a plant-derived natural product, isococculidine. The potential energy distribution (PED) has been assigned to each of the vibrational bands observed in FT-IR and FT-Raman spectra. The reduced density gradient (RDG) analysis was used to demonstrate the non-covalent interactions (NCI). Natural bond orbital (NBO) study revealed that the benzene ring's hyper-conjugative interactions were primarily responsible for the molecular stability. The intramolecular charge transfer has been further verified by the HOMO-LUMO analysis. The molecular electrostatic potential (MEP) analysis signifies that the nucleophilic and electrophilic interaction sites are prone to oxygen of O1-CH3 and hydrogens of O2-CH3, respectively. The chemical activity and the toxicity of the molecule have been examined based on the calculated Mulliken charges, softness, hardness, and local reactivity parameters. The thermal properties like specific heat capacity, entropy and enthalpy which affect the drug's activities were studied. The large value of the first hyperpolarizability indicates its significant nonlinear optical (NLO) property. The molecular docking of isococculidine has been performed with nicotinic acetylcholine protein which deliberates the significant biological activity of the molecule.