Using a novel powder X-ray pattern refinement technique, DFT calculations and TEM, we reveal for the first time the three-dimensional structure of hybrid (R₄N)_xMoS₂ layered compounds. Both the precise coordinates of Mo and S atoms in the inorganic layer and the preferred positions of the organic cations relative to them are reported. The distorted geometry of the MoS₂ sheet is found to be the driving force behind the arrangement of cations within the organic layers. The refined atomic coordinates, confirmed by periodic DFT modeling, show octahedral Mo atoms arranged in zigzag chains and the S atoms following the Mo ones, forming “ridges” and “valleys” on the sheet surface. The size of alkylammonium cations is compatible with these valleys, leading to a strong preferred arrangement: the cations exclusively occupy the space between the ridges. This result allows predicting the layer structure and ultimately the composition of the hybrid compound depending on the cation structure. The reported features of the MoS₂ surface are important for understanding of MoS₂-based sensors and hybrid flexible conductors, both relying on charged sheets of MoS₂.