Here, we report the covalently conjugation of lanthanide doped NaGdF4:Yb3+, Er3+@NaGdF4 upconverting nanoparticles (UCNPs) on methylphosphonate functionalized silica nanospheres (pSi NPs) for in vivo upconversion luminescence (UCL), T1-weighted magnetic resonance (MR), and X-ray computed tomography (CT) multi-modality imaging. The nanocomposites (pSi@UCNPs) were synthesized by a facile ligand exchange strategy. The hydrophobic pSi@UCNPs were transferred into aqueous solution by surface coating Pluronic F127. The Pluronic F127 coated pSi@UCNPs (pSi@UCNPs@F127) exhibit excellent stability in biological medium, inappreciable cytotoxicity and negligible organ toxicity. The pSi@UCNPs@F127 also shows brighter UCL, and higher CT/MR enhancements than that of Pluronic F127 coated NaGdF4:Yb3+, Er3+@NaGdF4 UCNP. In detail, the capability of pSi@UCNPs@F127 as high performance contrast agents for in vivo multi-modality (UCL/MR/CT) imaging is evaluated successfully through small-animal experiments.