The natural product gels (NPGs) have attracted more and more interest of researchers for their improved pharmacological activity and material properties. The phenomenon of natural micromolecules capable of forming gels induced by solvents predicts that supramolecular natural products has a capacious prospect in medicine and drugs fields as self-assembled materials. Herein, a new supramolecular NPG based on pomolic acid (PA) has been reported firstly. The self-assembly morphology of this compound was characterized utilizing scanning electron microscopy (SEM), transmission electron microscope (TEM) and atomic force microscopy (AFM). Particularly, microrheology monitor was employed to record the entire gelation and collapse process for the first time. Furthermore, the gel forming process and self-assembled mechanism of PA has been investigated by a series of experimental work and molecular dynamics simulation. This new discovery of NPGs enlightened that natural compounds with self-assembly properties provided new insights to understand the integrative mechanism in Chinese herbal medicines.