Targeting delivery is a promising technique for the therapy of cancers. A molecule FA-EEYSV-NH2, which consists of target recognition site folic acid (FA), dipeptide linker, and peptide drug, was designed as a novel anticancer prodrug. The molecules could self-assemble into nanoparticles at pH 7.0 and nanofibers at pH 5.0. By the aid of pH-responsiveness, the self-assemblies were used purposefully as targeted vehicles of self-delivery prodrugs. The results of cell toxicity and internalization assays have proved that the self-assemblies have good cancer cell selectivity. The selection was mainly attributed to the pH-responsive structure transition of self-assemblies and the FA active-targeting effect. We hope that our work could provide a useful strategy for finely tuning the properties and activities of peptide-based supramolecular nanomaterials, thus optimizing nanomedicines with enhanced performance.