3-(3-Methoxybenzyl)-1-(3-methylbenzyl)-1H-benzo[d]imidazol-3-ium chloride (4) was synthesized and characterized by H-1 NMR, C-13 NMR, FT-IR, LC-MS/MS, and single-crystal X-ray diffraction. The single-crystal X-ray diffraction analysis revealed that compound 4 crystallizes in the triclinic P-1 space group, forming a planar benzimidazole core stabilized by hydrogen-bonding and pi-pi stacking interactions. Its cytotoxic activity was evaluated against breast (MCF-7), liver (HepG2), colon (DLD-1), lung (A549), and prostate (PC3) carcinoma cell lines, showing IC50 values ranging from 24.55 & micro;M (MCF-7) to 64.25 & micro;M (DLD-1). Density functional theory (DFT) and potential energy surface (PES) analyses identified four stable conformers, one being the most thermodynamically favorable. Molecular docking indicated favorable VEGFR2 binding (docking score: -8.5 kcal/mol), albeit lower than sorafenib (-12.0 kcal/mol). Frontier molecular orbital analysis revealed the highest occupied molecular orbital (HOMO) localization on the benzimidazole core, supporting nucleophilic potential, while the lowest unoccupied molecular orbital (LUMO) is mainly localized over the aromatic substituents, suggesting potential pi-pi stacking interactions. Molecular dynamics simulations showed that compound 4 maintains a stable binding conformation with limited fluctuations. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations indicated energetically favorable complexes, with stabilization mainly driven by hydrophobic/van der Waals interactions, whereas sorafenib benefits more from electrostatic contributions.