The present invention relates to a cell-penetrating peptide/fluorescence-labeled magnetic nanoparticle complex and the use thereof. More specifically, relates to a cell-penetrating peptide/fluorescence-labeled magnetic nanoparticle complex in which a cell-penetrating peptide is chemically linked to a fluorescence-labeled magnetic nanoparticle, such that fluorescence-labeled magnetic nanoparticle can be stably introduced directly into cells without endocytosis, and a composition for cell imaging containing the complex. The disclosed invention suggests an innovative therapeutic technology which shows high stability, maximizes the effect of imaging diagnosis through optimal targeting and minimizes side effects, unlike existing viral peptide transporters.