Single crystal of L-Histidine Nitrate monohydrate (LHNM) has been grown from aqueous solution by evaporation technique. A comprehensive investigation of the NIR FT-Raman and FT-IR spectra was carried out with the aid of normal coordinate analysis following the scaled quantum mechanical force field methodology supported by the density functional theory (DFT) computations to analyze the effects of intramolecular charge transfer on the geometries and the vibrational modes contributing to the linear electro-optic effect of the organic NLO material. Effect of protonation and hydrogen bonding interactions has been analyzed using structural analysis, natural bond orbital analysis, and spectral analysis. The HOMO-LUMO energy gap value suggests the possibility of charge transfer within the molecule. Hyperconjugative interactions responsible for second hyperpolarizabilities have been described by NBO and AIM analyses. Hirshfeld surface analysis reveals that the van der Waals H⋯H (32.3%) contact plays a significant role in crystal packing and that a variety of N–H⋯O intermolecular contacts and hydrogen bonds leads to the formation of intermolecular charge transfer occurring in LHNM. The nonlinear refractive index (n2), nonlinear absorption coefficient (β) and third-order nonlinear susceptibility (χ3) of LHNM have been determined by Z-scan technique, which points to its potential application in the field of optical limiting. The calculated value of laser damage threshold was 2.04 GW/cm2. © 2018 Elsevier B.V.