This study was to develop a codrug delivery system for targeting cancer therapy based on magnetic RNA nanoflowers (RNA NF). Compared with traditional nucleic acid structure, convenient separation can be achieved by introducing magnetic nanoparticle (MNP) into RNA NF. Folic acid (FA) modified MNP/RNA NF (FA/MNP/RNA NF) was used as a targeting nanocarrier with excellent biocompatibility to overcome the nonselectivity of MNP/RNA NF. And then, anticancer drug doxorubicin (DOX) and photosensitizer 5, 10, 15, 20-tetrakis (1-methylpyridinium-4-yl) porphyrin (TMPyP4) binding with RNA NF were used as codrug cargo models. RNA NF was first used for codrug delivery. So, imaging fluorescent tags, target recognition element, and drug molecules were all assembled together on the surface of MNP/RNA NF. The experimental results suggested that the treatment efficacy of codrug delivery platform (FA/MNP/RNA NF/D/T) was better than single-drug delivery platform (FA/MNP/RNA NF/D). Besides, the FA/MNP/RNA NF was used as a probe for cancer cell detection. The limit of detection was 50 HeLa cells. In conclusion, the codrug delivery platform based on FA/MNP/RNA NF was a promising approach for the intracellular quantification of other biomolecules, as well as a diagnosis-therapy integrative system.