2,3-dimethylquinoxalinum-5-sulphosalicylate (MQSA) was synthesized and grown into single crystals by slowly evaporating the solvent in methanol at room temperature. According to the lattice parameters found by the SCXRD analysis method (a = 8.8031 (17) Å, b = 17.768(3) Å, c = 10.7979(16) and α = γ = 90°, β = 90.611 (7) °), the crystal belongs to monoclinic crystal system with the P21/n space group. Moreover, powder X-ray diffraction investigation supported the crystalline nature. The compound's UV–Vis spectra exhibited a CT-band with a wavelength maximum of 372 nm, as well as its NIR spectra revealed good optical transmittance in the visible region with a low cut-off wavelength of 376 nm and an optical band gap of 5.12 eV. Dual emission bands at 418 and 484 nm are observed in the PL emission spectra. The synthesized crystal was examined using FT-IR, FT-Raman, and NMR spectral methods. The crystal is thermally stable up to 274 °C, furthermore, TG-DTA and DSC methods were employed to study the degradation process. The second and third-order NLO efficiencies of the crystal was analyzed by Kurtz-Perry powder and Z-scan methods, respectively. The single crystal of MQSA is further studied through Hirshfeld surface analysis, fingerprint plots, and crystal voids analysis to understand the intermoleculiar interactions and individual atomic arrangements inside the crystal. The H…H and O…H/H…O interactions are greatly aided by crystal structure. Additionally, the quantum computational methods were used to assess several molecular level electronic properties, including molecular orbitals, molecular electrostatic potentials maps, linear polarizability and static third-order nonlinear optical (NLO) polarizability, which is a molecular-level NLO response property. The isotropic linear polarizability and NLO polarizability of MQSA are 29.99 × 10−24 esu and 28.45 × 10−36 esu, respectively, in the M06–2X/6–311G* method, which demonstrates the decent potential of the synthesized crystal for its use as NLO materials. Furthermore, the frontier molecular orbitals, molecular electrostatic potentials, and UV–Visible spectrum were calculated and discussed.