Our research shows the influence of the amount of deposited molecular layers on the morphology and optical properties of MoS2 nanostructures formed during the gas transport transfer of sulfur vapors to the hot zone of a reactor with metallic molybdenum and subsequent deposition on a mica substrate (muscavite). Our previous experience has shown that the temperature of gas transport synthesis of MoS2 nanolayers should not exceed 800◦C. By this time, we obtained MoS2 nanostructures of various thicknesses, starting from the monomolecular layer, in the temperature range of 525-600◦C. Results of research using atomic force microscopy AFM, optical absorption spectroscopy and Raman spectroscopy of MoS2 nanostructures of different thickness show that in the range of 525-600◦ C it is possible to obtain MoS2 monomolecular layers containing trigonal domains with D3h symmetry and having a band gap of 1.84 eV at a straight band optical transition with the formation of excitons at room temperature. The thickness of one molecular layer of MoS2 is equal to 0.625 nm. The two-layer films obtained under the same conditions contain domains of hexagonal symmetry D6h of micron sizes. In some areas of such films the top layer of MoS2 is folded into nanotubes several tens of microns long. With an increase in the number of deposited molecular layers, small trigonal domains self organize during growth into quantum dots of average diameter of about 50 nm, located at medium distances100-200 nm from each other. The next step in self-organization is formation of fractal-like structures of MoS2 with trigonal and hexagonal fragments. In the Raman spectra of these structures, the values of the modes of intra-layer and inter-layer vibrations E1 2g (377.5 cm−1) and A1 g (403.8 cm−1) differ not only from the corresponding values of the modes of the monomolecular layer, but also from all known values of bulk samples. The frequency of the intra- layer mode in these samples E1 2g has the lowest of all known values and is due to the intermediate dimension of the fractal substructures between 2D and 3D.