An organic complex derived from 2,6-diaminopyridinium hydrogen malonate (DAPMAL) was studied for its crystal growth, structure and properties including its non-linear optical (NLO) behavior. Single-crystal X-ray diffraction (SXRD) confirmed a monoclinic crystalline structure with a C2/c (15) space group. Density functional theory (DFT) calculations using the B3LYP/6311G(d, p) approach revealed significant hyperpolarizability indicative of strong NLO behavior. The natural bond orbital analysis is performed to identify hydrogen bonding and charge transfer interaction. A combined experimental and theoretical quantum chemical calculation has been accomplished to examine the molecule’s geometry, vibrational wavenumber, electronic transition, and NLO activity. Molecular electrostatic potential and are carried out to identify chemical reactivity and charge transfer interaction. The HOMO–LUMO energy gap for DAPMAL was calculated to be 5.926 eV at the B3LYP/6-311G(d,p) level of theory. The hole–electron analysis was performed to determine the type of excitation. Reduced density gradient is performed to identify the hydrogen bonding, steric, and van der Waals interactions. Thermal analysis (TG–DTA) shows thermal stability at 185 ℃ and decomposition patterns, while SEM–EDX is used to find the material’s purity and crystalline nature. UV–visible spectroscopy demonstrated transparency with a lower cutoff wavelength of 210 nm and fluorescence spectroscopy revealed 628 nm shows red emission. The Z-scan technique further validated 3.49E-06 the compound’s NLO potential for DAPMAL.