Hexagonal molybdenum oxide (h-MoO₃) micro-rods were synthesized through a facile hydrothermal method. Thermogravimetric and differential thermal analysis (TGA-DTA) of the sample, over temperatures ranging from 30°C to 700°C, was carried out to analyze the phase transition characteristics and thermal stability. The effect of post-thermal treatment on the structural, morphological, and optical characteristics of as-prepared samples were investigated in detail. X-ray diffraction (XRD) patterns of the sample confirmed the formation of h-MoO₃, and the presence of hexagonal-shaped micro-rods were observed through scanning electron microscopy (SEM). The crystalline phase was transformed to a thermodynamically stable orthorhombic structure (α-MoO₃) on thermal treatment, with the micro-rods transformed to flake-like morphology. Elemental composition was confirmed through energy dispersive x-ray spectroscopy (EDS) and x-ray photoelectron spectroscopy (XPS). Band gap energy estimated from the absorption spectra lies in the range 2.70–2.94 eV. The material exhibited a superior irreversible thermochromic property, which has been observed as color bands, in the visible to NIR region of the absorption spectra. The phenomenon was well explained with the support of the XPS scan for the Mo-3d and O-1 s states. Furthermore, the photoluminescence (PL) spectra, at an excitation of 330 nm (3.76 eV), showed five emission peaks centered between 360 nm and 550 nm, with enhanced intensity on thermal treatment. The physico-chemical characteristics revealed that the material can be applicable in thermo-chromic smart windows and as host material in light-emitting diodes.