Good quality single crystals of 2-amino-4,6-dimethylpyrimidine 4-nitrophenol (AMP4N) were successfully grown by slow evaporation solution technique (SEST) at room temperature using methanol as solvent. The grown crystal was subjected to single crystal XRD (SXRD) and its structure was solved by the direct method using SHELXS program and refined using SHELXL program. The Hirshfeld surfaces analysis was carried out to define theoretically electron density boundary surfaces between the molecules in a grown crystal, which are useful to analyze and view the intermolecular interactions. The powder XRD (PXRD) was carried out to identify the crystalline planes and its strain was also calculated by the Williamson–Hall equation. 13C and 1H NMR were recorded to interpret the environment of the molecular structure of the AMP4N crystal. Functional groups of AMP4N crystal were confirmed by Fourier transform infrared (FTIR) spectral analysis. The optical quality of the grown crystal was analyzed by UV–Vis NIR spectral analysis. The grown crystal has good optical transparency in the range 410–1100 nm. The thermal behaviour of the crystal has been investigated by thermogravimetric and differential thermal analysis (TG-DTA). Chemical etching study was carried out and the etch pit density (EPD) was calculated. The laser damage threshold (LDT) was measured under single-shot mode using an Nd: YAG laser at 532 nm. The third-order nonlinear optical properties such as refractive index (n2), absorption coefficient (β) and susceptibility (χ(3)) were studied using the Z-scan technique at 532 nm with a continuous wave (CW) solid-state laser.