In this project, a one-step hydrothermal process is used to synthesize MoS2 photocatalysts of different morphology and shape. The photocatalytic degradation of MB (methylene blue), MG (malachite green), and RhB (rhodamine B) is carried out under visible light irradiation. It is observed that the MoS2 nanoflowers exhibit the highest degradation as compared to MoS2 nanosheets. Photocatalytic stability analysis performed on MoS2 nanoflowers showed excellent stability in MB, MG, and RhB and degradation percentage after four consecutive cycles. The flower type morphology of nanostructure also increases the adsorption–desorption of organic dyes on the active sites and reduces the charge recombination. Overall, the surface morphology with exposed edge sites substantially affects the photocatalytic activity, contributing an essential model for designing a more effective photocatalyst. The free radicals trapping experiment demonstrated that photogenerated hydroxyl radicals contributed a major role in the degradation of organic pollutants.