Non-platinum electrodes for photoelectric devices are challenging and attractive to the scientific community. A thin film of molybdenum disulfide (MoS2) was prepared on substrates coated with fluorine-doped tin oxide (FTO) to substitute the platinum counter electrode (CE) for dye-sensitized solar cells (DSSCs). Herein, we synthesized layered and honeycomb-like MoS2 thin films via the cyclic voltammetry (CV) route. Thickness and morphology of the MoS2 thin films were controlled via the concentration of precursor solution. The obtained results showed that MoS2 thin films formed at a low precursor concentration had a layered morphology while a honeycomb-like MoS2 thin film was formed at a high precursor concentration. Both types of MoS2 thin film were composed of 1T and 2H structures and exhibited excellent electrocatalytic activity for the I3–/I− redox couple. DSSCs assembled using these MoS2 CEs showed a maximal power conversion efficiency of 7.33%. The short-circuit value reached 16.3 mA·cm−2, which was higher than that of a conventional Pt/FTO CE (15.3 mA·cm−2). This work reports for the first time the possibility to obtain a honeycomb-like MoS2 thin film morphology by the CV method and investigates the effect of film structure on the electrocatalytic activity and photovoltaic performance of CEs for DSSC application.