We have constructed a multifunctional nanoprobe with sensing and imaging properties by using hollow mesoporous silica coated upconversion nanoparticles (UCNPs) and Hg(2+) responsive ruthenium (Ru) complex. The Ru complex was loaded into the hollow mesoporous silica and the UCNPs acted as an energy donor, transferring luminescence energy to the Ru complex. Furthermore, polyethylenimine (PEI) was assembled on the surface of mesoporous silica to achieve better hydrophilic and bio-compatibility. Upon addition of Hg(2+), a blue shift of the absorption peak of the Ru complex is observed and the energy transfer process between the UCNPs and the Ru complex was blocked, resulting in an increase of the green emission intensity of the UCNPs. The un-changed 801 nm emission of the nanoprobe was used as an internal standard reference and the detection limit of Hg(2+) was determined to be 0.16 μM for this nanoprobe in aqueous solution. In addition, based on the low cytotoxicity as studied by CCK-8 assay, the nanoprobe was successfully applied for cell imaging and small animal imaging. Furthermore, when doped with Gd(3+) ions, the nanoprobe was successfully applied to in vivo magnetic resonance imaging (MRI) of Kunming mice, which demonstrates its potential as a MRI positive-contrast agent. Therefore, the method and results may provide more exciting opportunities to afford nanoprobes with multimodal bioimaging and multifunctional applications.