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A metastable, not naturally occurring 1T polymorph of molybdenum disulfide, resulting from a negative charge transfer onto the layers of stable 2H polymorph present in the mineral molybdenite, holds great promises for electrocatalysis and other applications. We showed that stabilization of 1T-MoS2 sheets can be achieved by their incorporation into hetero-layered nanocrystals (NCs) obtained through self-assembly of the negatively charged MoS2 monolayers resulted from chemical exfoliation of LiMoS2 crystals and the organic cationic species derived from alkyl(aryl)amine, alkylimidazolium or aminonaphthalene molecules. The crystal structure of the assembled NCs was determined due to combination of PXRD pattern analysis with DFT calculations and TEM results [1,2,3]. The studies evidenced that the geometry of MoS2 layers in NCs belongs to 1T type, with the intra-layer ordering of octahedrally coordinated molybdenum atoms forming endless zigzag Mo-Mo chains in sulfide layers, and the sulfur atoms periodically displaced in the direction perpendicular to the layers to form nanoridges and nanovalleys alternating on the MoS2 sheet surface. The essential bonding interactions of the sulfide sheets with aliphatic, aromatic or hydrogen bond donor fragments of organic molecules (CH…S, C…S, N…S, NH…S) were revealed in the obtained NCs by QTAIM analysis of calculated electron density distribution. These interactions were found to govern the positioning of the organic molecules so as they follow the sulfide sheet nanorelief. The cation – MoS2 interactions also have an important influence on the overall stability of the 1T-MoS2 structure, resulting in significant increase in the temperature of its phase transformation to conventional 2H-MoS2 counterpart.