Multimodal imaging probes have attracted wide attention and have potential to diagnose diseases accurately because of the complementary advantages of multiple imaging modalities. However, intractable issues remain with regard to their complicated multi-step fabrication for hybrid nanostructure and interference of different modal imaging. In the present study, we present, for the first time, T₁ and T₂-weighted magnetic resonance imaging (MRI) of ultrasmall Mn²⁺-doped NaNdF₄ nanocrystals (NCs), which can also be used simultaneously for second near infrared (NIR-Ⅱ) fluorescence and computed tomography (CT) imaging, thus enabling high-performance multimodal MRI/NIR-Ⅱ/CT imaging of single NaNdF₄: Mn NCs. The NaNdF₄: Mn was demonstrated as a nanoprobe for in vitro and in vivo multimodal MRI and NIR-Ⅱ fluorescence imaging of human mesenchymal stem cells. The results provide a new strategy to simplify the nanostructure and preparation of probes, based on the features of NaNdF₄: Mn NCs, which offer highly efficient multimodal MRI/NIR-Ⅱ/CT imaging.