Heterocyclic compounds, including isoquinoline derivatives with oxygen and sulfur groups, are important in anticancer drug discovery. They show strong biological activity and structural diversity. Medicinal studies, molecular docking, and DFT analysis help understand their effectiveness, binding ability, and stability. For this purpose, we synthesized a new isoquinoline derivative (AHIC). Its structure was verified by single-crystal X-ray analysis. The compound's geometry, FMO, and MEP were analyzed using DFT, supported by experiments. Hirshfeld surface, 3D energy framework, NLO, and NBO analyses identified hydrogen bonds affecting crystal packing. The compound shows strong NLO properties, high charge transfer, and stability, suggesting potential as an anticancer drug. The medicinal potential of AHIC was evaluated through an in silico approach in which it proved to be an effective candidate for anticancer drug development as it efficiently bound with the target substrates with binding energies of −6.87 and −6.31 Kcal/mol along with ligand efficacies of −0.24 and −0.22 Kcal/mol against Tdp1 and EGFR substrates. The MD simulation studies showed the stability of the ligand-protein complexes by calculating the RMSD for the conformation changes in the protein structure over the simulation trajectory and RMSF and SASA parameters for the accessibility of water molecules in the cell-like environment.