Due to various applications in tissue engineering, regenerative medicine, protein separation, cell therapy, drug carriers, and sensors, supramolecular hydrogels based on molecular self-assembly of peptide derivatives have recently attracted widespread attention. Supramolecular hydrogel is a three-dimensional network formed by non-covalent bond forces that have highly biocompatible for many biological systems. Self-assembling peptides have four categories: small-molecule peptides, peptide amphiphiles, amphipathic peptides, and surfactant-like peptides. Recently, small molecule peptides have attracted much attention due to their simple structure, tunable composition, and unique supramolecular structure. This review provides a general introduction for researchers interested in exploring supramolecular hydrogels as biomaterials. The molecular design of small-molecule peptides and their applications in bio-medicine are also discussed.