Luminescence nanothermometry has attracted much attention as a non-contact thermal sensing technique. However, it is not widely explored for in vivo applications owing to the low transparency of tissues for the light to be used. In this study, we performed biological temperature sensing in deep tissues using β-NaYF4 nanoparticles co-doped with Yb3+, Ho3+, and Er3+ (NaYF4: Yb3+, Ho3+, Er3+ NPs), which displayed two emission peaks at 1150 nm (Ho3+) and 1550 nm (Er3+) in the >1000 nm near-infrared wavelength region, where the scattering and absorption of light by biological tissues are at the minimum. The change in the luminescence intensity ratio of the emission peaks of Ho3+ and Er3+ (IHo/IEr) in the NaYF4: Yb3+, Ho3+, Er3+ nanothermometer differs corresponding to the thickness of the tissue. Therefore, the relationship between IHo/IEr ratio and temperature needs to be calibrated by the depth of the nanothermometer. The temperature-dependent change in the IHo/IEr was evident at the peritoneal cavity level, which is deeper than the subcutaneous tissue level. The designed experimental system for temperature imaging will open the window to novel luminescent nanothermometers for in vivo deep tissue temperature sensing.