Targeted photodynamic therapy is considered superior to conventional photodynamic therapy due to the enhanced uptake of photosensitizers by tumor cells. However, porphyrin-based photodynamic therapy is still limited due to the low hydrophilicity, poor biocompatibility and susceptibility to quenching of photosensitizers. Herein, we report cyclodextrin-activated porphyrin-DNA nanofibers with AS1411/Hemin toeholds, which enable targeted cancer cells recognition and catalytic oxygenation for enhanced photodynamic therapy. The nanofibers are formed through the self-assembly of the host–guest complex of cyclodextrin and porphyrin-DNA amphiphiles, and can be further functionalized on the surface with AS1411/Hemin. AS1411/Hemin can specifically target nucleolin-overexpressing cancer cells and catalyze conversion of excessive H2O2 into O2 within tumor cells, thereby alleviating tumor hypoxia and further cascaded enhancing PDT efficacy. These results suggest that the programmable and multifunctional nanofiber provided an effective nanoplatform for enhanced and targeted photodynamic therapy.