Finding a low-cost material with properties that satisfy the requirement of energy crises and a cleaner environment is imperative. In this work, by employing a one-step hydrothermal method, we demonstrate the successful synthesis of a phase-engineered (1T/2H) MoS₂/α-MoO₃ heterostructure nanoflower at a temperature of 200°C. We tuned the 1T-rich phase of MoS₂ to the 2H-rich phase by optimizing the synthesis time. Additionally, the morphology and crystallinity of the as-prepared samples were characterized through scanning electron microscopy, X-ray diffraction, and high-resolution transmission electron microscopy. The MoS₂ phase and the presence of α-MoO₃ were analyzed through Raman and X-ray photoemission spectroscopy. The sample prepared at 16 h attained a high surface area of 37.97 m²g⁻¹, and 97% of the RhB dye with the initial concentration of 47.9 mg L⁻¹ was removed within 10 min through adsorption; this is the highest known removal efficiency reported in the literature. As a hydrogen evolution reaction (HER) electrocatalyst in an acidic solution, the sample prepared at 12 h exhibited highly efficient catalytic action by achieving a lower overpotential of 232 mV at a current density of 10 mA cm⁻², which is comparable with previously reported HER catalysts based on MoS₂. Moreover, this sample reached a lower Tafel slope of 81 mV dec⁻¹ and was stable over 1000 cycles. This superior dye degradation ability and these highly efficient electrocatalytic properties are attributable to the heterostructure nanoflower morphology.