We designed and synthesized NaYF4:Yb,Tm@LiLuF4:Nd core-shell nanoparticles, which can emit at ∼800 nm under 980 nm excitation and at ∼1060 nm under 808 nm excitation, simultaneously having an upconversion and downshifting mechanism for near-infrared (NIR) emission. After surface modification with sodium citrate, the soluble nanoparticles were used in the in vitro NIR luminescence imaging to compare the penetration depth and the scattering of tissue. Furthermore, to determine the differences between the upconversion and downshifting fluorescence for biological imaging, the soluble nanoparticles also were operated on the aforementioned two modes for in vivo imaging.