In this article, a variety of well defined, highly symmetrical, and nanostructures of WO3 based materials were successfully synthesized through facile hydrothermal method at different reaction time 12, 18, 24, 30, and 36 h respectively. The as synthesized samples were characterized using SEM, EDX, XRD, BET, UV–Vis, and PL to investigate the morphology, purity and elemental composition of material, structural properties, surface area and optical properties respectively. SEM reveals that morphology of nanostructured materials have been significantly affected by varying the hydrothermal duration. XRD peaks show the monoclinic and hexagonal phase for a different reaction time, whereas EDX confirmed the purity of material. UV–Vis and PL confirmed the band edge position and high degradation rate. The as-prepared nanostructures also showed a very high specific surface area and proved an exceptional ability to eliminate organic pollutants. Experimental results showed that the efficient photocatalytic activity of methylene blue can be attributed to the carefully controlled hierarchical WO3 structures by modulating the surface morphology confirmed by PL and photocatalytic activity test as well.