The invention discloses a fat tertiary diurea micromolecule gelling agent and a thixotropic molecular gel thereof. The gelling agent molecules contain fatty tertiary amines and ureido fragment, and can be dissolved into dichloromethane, tetrahydrofuran, acetone, benzene, toluene, paraxylene, ortho-xylene, xylene, styrene, butyl acrylate, silylated agent through heating treatment, and when room temperature cools down, a stable shearing thixotropic molecule gel can be formed; sol-gel phase transition accelerates and sol-gel phase transition is reversible by 100%, and the phase transition can be repeated for at least 15 times. Organic carboxylates are added to the molecular gel, so that the thixotropic molecular gel with higher rheological properties can be obtained. These molecular gels are expected to be used as benign media for preparing flawless crystal of organic or inorganic materials.