Gene therapy is a novel therapeutic method and widely used for treating numerous diseases. However, the utilization of suitable materials for specifically and effectively delivering therapeutic oligonucleotides (ODNs) into a targeted site remains a great challenge. Regarding this, by possessing the capabilities of high loading rate, good stability, targeting ability and biological barrier penetration, peptide-based nanomaterials are developing rapidly and becoming a new trend in the application of gene therapy. In this review, a variety of peptide-based nanomaterials designed for gene therapy are briefly demonstrated, focusing on their main constituents in terms of three aspects: (1) small molecules, (2) nanoparticles and (3) polymers. Using peptide-based nanomaterials, a controlled gene delivery process can be achieved and directly monitored in a real-time mode. In future work, different designs of peptide-based nanomaterials need to be explored for higher gene transfection efficiency and a better therapeutic effect. In the end, some challenges and deficiencies are mentioned for bringing more attention to accelerate the research of peptide-based nanomaterials.