In this study, we compare and investigate both microscopic molecular packing and mesoscopic morphogenetic behavior in two-dimensional (2D) organized films/three-dimensional (3D) solids of three kinds of Gemini-type diamide surfactants that systematically differ in terms of their chemical structure. The gelation of the surrounding medium is promoted by growing crystalline nanofibers of these surfactants, and the disappearance of these nanofibers and solvent reflow are caused by the application of a force on the corresponding gel because these surfactant molecules are considered potential thixotropic agents. The layer structure and sub-cell in the 3D crystals of surfactants are formed by the association of van der Waals force and hydrogen bonding because the mechanism responsible for crystalline nanofiber formation is intermolecular hydrogen bonding. In the monolayer on the water surface, only surfactant molecules having a hydroxyl group in the hydrophobic chain formed crystalline nanofibers. The introduction of hydroxyl groups into the hydrophobic chains also promoted a single-phase molecular conformation in 3D crystals. However, the absence of hydroxyl groups in the hydrophobic chain promoted the growth of the nanofibers in the cast film, whereas the introduction of hydroxyl groups in the hydrocarbons improves the thixotropic property itself. In addition, the epitaxial growth of nanofibers upon the addition of a growth aid was promoted by the absence of hydroxyl groups.