In this study, a complete investigation on molecular and vibrational structure of 2-aminopyrazinium 5-nitro-2-hydroxybenzoate (2APZ5NHB) crystal was analyzed. Single crystal XRD analysis confirms that the crystal has monoclinic crystal system (a = 13.3851(16) Å, b = 11.7318(13) Å, c = 7.9004(8) Å, β = 100.618(4)°) with P21/c space group. The usual $$R_{2}^{2}$$ R 2 2 (8) ring motifs are formed through two N–H···O hydrogen bonds. The N–H···O hydrogen bonding interactions were quantitatively analyzed by Hirshfeld surface and fingerprint analyses. 2APZ5NHB has been characterized by FTIR, Raman, UV–Vis spectroscopy and TG/DTA analysis experimentally and the corresponding DFT calculations were done theoretically. The optimized molecular geometry of 2APZ5NHB and their corresponding vibrational assignments are correlated. UV–Visible transmission spectrum shows the cutoff wavelength around 340 nm. Thermal analysis revealed that 2APZ5NHB crystal was thermally stable up to 135 °C. The electronic band gap and the first-order hyperpolarizability calculated which signifies the 2APZ5NHB crystal for NLO applications.