This study provides a detailed charge density distribution analysis of 6-methyl-2-thiouracil crystals together with comprehensive energetic investigations. The findings constitute a link between crystal network features, electronic structure, molecular motif interaction energy, and crystal morphology. Our results revealed agreement between the topologically estimated hydrogen bond energy and the computational values. It also occurred that the methyl group and sulfur atom significantly affect crystal packing and contribute to a variety of intermolecular contacts. Nevertheless, the strongest interactions observed in the crystal structure are of electrostatic type. It is well reflected in the generated molecular electrostatic potential surfaces of the complementary character. Additionally, simple analysis of the interslab interaction energies and surface energy values led to a rough explanation of the crystal elongation direction and preferably created facets, such as the well-developed \010\ crystal form. It should be also noted that complex investigations of the charge density distribution revealed significant residual peaks next to the sulfur atom, neither reliably modeled, nor justified by theory. These could be explained by the presence of a small percentage of the oxo-thiol tautomeric form in the crystal or by the S center dot center dot center dot S interactions across the crystal lattice (S-S bridge formation, etc.); however, no binding conclusions were drawn.