MoS2 is one of the most attractive transition metal dichalcogenide (TMD) materials for electronic applications due to its unique properties. In this study, MoS2 nanoflakes were synthesized by the metal-organic chemical vapor deposition (MOCVD) method on various substrates including glass and alumina. The substrate effects on the morphology and structural properties of MoS2 nanostructures were evaluated by different techniques including field-emitting scanning electron microscope (FE-SEM), energy dispersive spectrum (EDS), X-ray diffraction (XRD), photoluminescen and Raman spectra. The results indicate that MoS2 nanoflakes could be synthesized effectively on both glass (MoS2/glass) and alumina (MoS2/Al2O3) substrates. However, the morphology and many structural properties of MoS2 nanoflakes are modified significantly when changing the substrates. The Mo/S atomic ratio changes from 0.62 to 0.45 for MoS2/Al2O3 and MoS2/glass, respectively. In addition, MoS2/Al2O3 reveals a less uniform structure along with thicker edges of MoS2 nanoflakes in comparison to that of MoS2/glass. For application, as-synthesized MoS2 nanoflakes could be considered as a potential candidate for selective H2S detection owing to the presence of dangling bonds in MoS2 nanoflakes as well as the differences in the adsorption ability and charge transfer between target gases and MoS2.