Dual-modal imaging by combining magnetic resonance (MR) and near-infrared (NIR) fluorescence can integrate the advantages of high-resolution anatomical imaging with high sensitivity in vivo fluorescent imaging, which is expected to play a significant role in biomedical researches. Here we report a dual-modality imaging probe (NIR/MR-MSNs) fabricated by conjugating NIR fluorescent heptamethine dyes (IR-808) and MR contrast agents (Gd-DTPA) within highly aminated mesoporous silica nanoparticles (MSNs-NH2). The dual-modality imaging probes NIR/MR-MSNs possess a size of ca. 120 nm. The NIR/MR-MSNs show not only near-infrared fluorescence imaging property with an emission peak at 794 nm, but also highly MR T1 relaxivity of 14.54 mM−1 s−1, which is three times more than Gd-DTPA. In vitro experiment reveals high uptake and retention abilities of the nanoprobes, while cell viability assay demonstrates excellent cytocompatibility of the dual-modality imaging probe. After intratumor injection with the NIR/MR-MSNs, MR imaging shows clear anatomical border of the enhanced tumor region while NIR fluorescence exhibits high sensitive tumor detection ability. These intriguing features suggest that this newly developed dual-modality imaging probes have great potential in biomedical imaging.