A conventionally grown organic nonlinear optical crystal bisguanidinium isophthalate monohydrate was structurally investigated using single crystal X-ray diffraction study. The lattice constants, supramolecular arrangements and the hydrogen bond formation of the title compound confirm the formation of novel organic crystalline material. The various functional groups present in the crystalline material were resoluted by employing FT-IR spectral analysis. The wide-range optical transparency of the compound in the entire visible region ensures the optical quality with a lower cut-off wavelength at 298 nm was analysed experimentally using UV–vis–NIR spectrometer. The support of DFT was scrutinized to report the optimized structure, electronic state properties, hyper-conjugative interactions and frontier molecular energy gap of the bisguanidinium isophthalate compound. The charge transfer mechanism of bisguanidinium isophthalate compound from isophthalic acid to guanidine compound was also interpreted using theoretical DFT. The computational evaluation of charge stabilities as a result of charge delocalization was construed with the ratification of natural bonding orbital (NBO). The assessed thermal stability of bisguanidinium isophthalate crystal is 120 °C which was analysed by thermogravimetric and differential thermal analyses. To determine the third-order nonlinear optical property with quantitative results of nonlinear refractive index, nonlinear absorption coefficient and optical susceptibility was ascertained using Z-scan technique. © 2019 Elsevier B.V.