Hexagonal molybdenum oxide (h-MoO₃) nanocrystals with a flower-like hierarchical structure have been successfully synthesized by a solution based self assembly route. The as-synthesized h-MoO₃ was recognized as a photocatalyst for the photocatalytic degradation of methylene blue (MB) under various experimental conditions. Initially, the as-synthesized h-MoO₃ was characterized by different physico-chemical techniques in order to study and reveal the structural, functional, morphological, and optical properties. The results indicated that the photocatalyst has a hexagonal crystal structure with an average crystallite size of 46 nm. The morphology analysis has proved that the h-MoO₃ comprises one dimensional (1D) rods with a hexagonal cross section. The possible formation mechanism is proposed as a self assembly process for nucleation and an Ostwald ripening mechanism for particle growth. The optical band gap investigation showed that the E_g value of h-MoO₃ (2.94 eV) lies in the visible region and can be an appropriate candidate for visible light photocatalytic application. Furthermore, the experimental observations demonstrate an excellent photocatalytic performance of h-MoO₃ in the degradation of MB under visible light irradiation.