In this work, vertically aligned MoS2 nanoflakes on Ti foil have been successfully prepared by different hydrothermal methods (using water or ammonia solvent) towards fabricating photoanodes with high visible light photoelectrochemical performance. The few-layered MoS2 (4-10 nm) nanoflakes electrode grown in water exhibits unprecedented higher photocurrents under visible light irradiation, and the stability of the few-layered MoS2 electrode was markedly enhanced by annealing the sample at 300 degrees C. The underlying mechanisms accounting for the superior photoelectrochemical performance of the few-layered MoS2 nanoflakes are found to be correlated with their phase, crystallinity, length, number of layers and photon absorption efficiency etc. Furthermore, the photoelectrochemical degradation of organic chemicals including rhodamine B dye, 4-chlorophenol, chlorpyrifos and ciprofloxacin selected as different types of pollutants in wastewater was evaluated and compared utilizing the few-layered MoS2 nanoflakes photoanode. The photoelectrochemical degradation efficiency is strongly influenced by the molecular structures and properties of pollutants and experimental condition parameters such as solution pH, oxygen concentration and applied bias potential. The available high electron cloud density sites induced by the electron-withdrawing functional groups in different substrates might determine the substrate-specific PEC degradation efficiency. The present MoS2-based PEC system could be further optimized for efficient degradation of recalcitrant pollutant like ciprofloxacin.