Peptides are widely found in natural organisms and play a variety of biological functions in human body. Compared with traditional materials, peptides have lower immunogenicity and better biocompatibility, which makes them ideal biological materials. Self-aggregating peptide is a kind of peptide chain that can be assembled by covalent binding of monomers under physiological or pathological conditions. Their advantages include the ability to aggregate by themselves and their low immunogenicity and biocompatibility as peptides. Therefore, self-aggregating peptides have various potential applications in biology and medical field. Since self-aggregating peptide can self-assemble into insoluble particles under certain conditions, wrapping the target protein with self-aggregating peptide can achieve the purpose of protein purification by simple centrifugation. This method is superior to the existing protein purification methods, since the experimental efficiency and cost can be optimized. Moreover, self-aggregating peptides, because of their peptide nature, do not elicit strong immune responses. Thus, self-aggregating peptides can be loaded with a large number of drugs and can be biodegraded into unharmful products which can be smoothly absorbed by the human bodies. The self-aggregated peptide loaded subunit vaccine can successfully induce and enhance immune response without adverse reactions, which is superior to existing immune adjuvants. Self-aggregated peptide also helps keeping the vaccine active for a long time and effectively reduce the cost of vaccine promotion. Select self-aggregating peptides that can be cleaved under pathological conditions to load drugs can help achieve drug targeting. In addition, the self-aggregating peptides loaded with drugs can be stored in specific sites for a long time, so that it does not require repeated dosing, thus improving the efficiency of drug administration. In this paper, the design of peptide self-assembly based solutions and their different biomedical applications are summarized, and their future prospects are prospected.