Molecular design and biomimetic/bioinspired synthesis provide facile ways for the construction of functional nanomaterials for various applications. Peptide-based functional nanomaterials with ideal morphology and functions can be obtained through the design of peptide sequences, regulation of molecular self-assembly, biomimetic synthesis, and hybridization with other functional nanoscale building blocks. In this review, we present a progress report on the combination of peptide self-assembly and biomimetic synthesis for tailoring the structure and functions of peptide nanomaterials aiming to biomedical applications. Through structural and functional tailoring, peptide-based nanomaterials exhibit enhanced chemical, physical, and biological properties, which greatly promote their potential applications in biomedical fields, including biosensors, bioimaging, photothermal/photodynamic therapy, tissue engineering, drug/gene delivery, and antibacterial materials. This interesting research topic could be promoted by discovering more peptide sequences, investigating the self-assembly behavior of peptides, simulating the internal driving factors of peptide self-assembly, and accurately controlling the functions of peptides to prepare peptide-based hybrid nanomaterials, which are beneficial to design and fabricate functional biocompatible nanosystems for clinical biomedicine.