Efficient deep-penetrating red upconversion luminescent nanoparticles with ultra-small size are promising biological temperature probes. Herein, bright red upconversion luminescence are achieved in NaErF4@NaYF4 core-shell nanoparticles under multi-wavelength excitation of 808 nm, 980 nm, and 1550 nm. The core-shell structure engineering is constructed to minimize energy dissipation by surface quenchers. Furthermore, the established model explains the temperature dependence of thermally coupled energy levels in detail, confirming that the non-radiative relaxation is responsible for the quenching processes. Based on the luminescence intensity ratio technique, optical temperature sensing characteristics of thermally coupled (2H11/2/4S3/2) and non-thermally coupled energy levels (4F9/2/4S3/2) are investigated under the excitation of a relatively safe near-infrared wavelength for 1550 nm. The thermometer can maintain a maximum sensitivity of 35 × 10−3 K−1 over the entire temperature measurement region by fitting the non-thermally coupled energy levels, which is conducive to temperature monitoring in vivo due to high sensitivity and relatively safe excitation wavelength.