In this study, a simple hydrothermal method was employed to synthesize 3D flower-like MoS2 nanostructures. The influence of different synthesis temperatures on the structural, electronic, optical and morphological properties of the MoS2 nanostructures was thoroughly investigated, and the optimal temperature was identified as 220 °C. Additionally, we conducted further optimization to determine the most suitable reaction time, which was found to be 24 h. The characterization of the synthesized MoS2 nanostructures, employing various techniques such as X-ray diffraction, Raman spectroscopy, Mott-Schottky analysis, UV–vis-NIR spectroscopy and field emission scanning electron microscopy, unveiled well-defined crystallinity, reduced thickness and uniform morphology, under the optimized conditions. Notably, as the temperature increased from 180 °C to 220 °C, the band gap of MoS2 nanostructures exhibited a notable increase from 1.72 to 2.35 eV. The Mott-Schottky analysis further confirmed our findings, revealing lower values of flat band potential and carrier concentration for the optimized temperature (220 °C), indicative of higher crystallinity with fewer defects. These comprehensive findings not only underscore the significant impact of temperature and time on the properties of MoS2 nanostructures but also hold promising implications for diverse applications, including sensing, energy storage, as well as photocatalysis for hydrogen evolution reactions and organic pollutant degradation.