2D-layered nanostructure-based advanced coatings are the most recent advancement in the field of advanced oxidation processes. Effective charge separation is one of the key parameters in enhancing the photodegradation ability of 2D-layered nanostructures. We report the cost-effective hydrothermal synthesis of MoS2 thin films on conductive ITO substrates with tunable morphology. Scanning electron microscopy studies manifested the modulation in the morphology of MoS2 thin films and confirmed the presence of spherical, thread, and sheet-like nanostructures under the evolution of precursor concentration. UV–visible absorption spectroscopy revealed the modulation in the optical absorption and effective bandgap narrowing with the changes in the surface morphology. The estimated bandgap value of MoS2 thin film samples varies from 1.82 to 1.69 eV. PL spectroscopy and electrochemical studies display the morphology-dependent charge separation behavior and confirm that the lowest recombination rate is attained by thread-like MoS2 nanostructures. Raman spectroscopy and x-ray photoelectron spectroscopy confirms the 2H phase of MoS2 thin films. MoS2 thin films with thread-like structures are found to be the most efficient for sunlight-induced photodegradation activity as compared to other MoS2 samples. Thread-like MoS2 structures containing MoS2 thin film with the highest charge transport properties decompose 85% of 5 µM methylene blue molecules and 90.4% of 5 µM rhodamine B molecule solution in 40 min and 80 min, respectively, under natural sunlight. The prominent charge separation effects on the enhanced photodegradation capabilities of MoS2 thin films due to distinct variations in morphology, which have not been reported till now, are explored precisely.