Self-assembling peptide-based nanodrug delivery systems (NDDs), consisting of naturally occurring amino acids, not only share the advantages of traditional nanomedicine but also possess the unique properties of excellent biocompatibility, biodegradability, flexible responsiveness, specific biological function, and synthetic feasibility. Physical methods, enzymatic reaction, chemical reaction, and biosurface induction can yield versatile peptide-based NDDs; flexible responsiveness is their main advantage. Different functional peptides and abundant covalent modifications endow such systems with precise controllability and multifunctionality. Inspired by the above merits, researchers have taken advantage of the self-assembling peptide-based NDDs and achieved the accurate delivery of drugs to the lesion site. The present review outlines the methods for designing self-assembling peptide-based NDDs for small-molecule drugs, with an emphasis on the different drug delivery strategies and their applications in using peptides and peptide conjugates.