A novel method of rare-earth cation-assisted ligand assembly has been developed to provide upconversion nanophosphors with T(1)-enhanced magnetic resonance (MR), radioactivity, and targeted recognition properties, making these nanoparticles potential candidates for multimodal bioimaging. The process of modifying the surface of the nanophosphors has been confirmed by transmission electron microscopy, X-ray powder diffraction, X-ray photoelectron spectroscopy, proton nuclear magnetic resonance, Fourier-transform infrared spectroscopy, energy-dispersive X-ray analysis, and so on. The versatility of this surface modification approach for incorporating functional molecules and fabricating fluorine-18-labeled magnetic-upconversion nanophosphors as multimodal bioprobes has been demonstrated by targeted cell imaging, in vivo upconversion luminescence, MR imaging, and positron emission tomography imaging of whole-body small animals.