Molecular imaging probes that enable seamless diagnoses of tumors in the preoperative and intraoperative stages could lead to surgical resection of tumors based on highly accurate diagnoses. Because iron oxide nanoparticles (IONPs) have high proton relaxivity and high molar extinction coefficients suitable for magnetic resonance imaging (MRI) and photoacoustic imaging, respectively, we planned to develop molecular imaging probes applicable to the pre- (MRI) and intraoperative (photoacoustic imaging) stages. Human epidermal growth factor receptor 2 (EGFR2; HER2) was selected as a target molecule, and we designed IONPs (20, 50, and 100 nm) conjugated with anti-HER2 moieties [whole IgG (trastuzumab), single-chain fragment variable (scFv), and peptide] for HER2-targeted tumor imaging. Among the probes tested, scFv-conjugated IONPs (scFv-IONPs) (20 nm) exhibited the highest binding affinity to HER2 (K=0.01 nM). An in vivo biodistribution study using In-labeled probes demonstrated that more scFv-IONPs (20 nm) accumulated in HER2-positive than in HER2-negative tumors, suggesting that the uptake of scFv-IONPs is HER2 specific. The scFv-IONPs (20 nm) showed high proton relaxivity and a probe concentration-dependent photoacoustic signal. In vivo MR/photoacoustic imaging studies using scFv-IONPs (20 nm) facilitated HER2-specific visualization of tumors. Furthermore, an iron-staining study demonstrated that the uptake of scFv-IONPs was notable only in HER2-positive tumors. These results suggest that scFv-IONPs (20 nm) may be useful for MR/photoacoustic dual imaging, which could achieve seamless diagnoses in the preoperative and intraoperative stages.