Luminescence thermometry technique, which utilizes the rare earth ions activated luminescent nanomaterials as sensing media, has presented great potential in various fields owing to its high spatial, temporal, and thermal resolutions. Nevertheless, the development of sensitive luminescent nanothermometers working in the biological window remains a challenge. Here, Tm3+-Yb3+ codoped NaYF4 nanocrystals, the excitation and emission wavelengths of which are both located within the near-infrared region, are investigated for optical temperature measurement via the fluorescence intensity ratio (FIR) approach. The thermal population and decay rates involved in the thermally coupled levels (3F2, 3 and 3H4) are verified to play an important role in regulating the thermal coupling status. The measurement sensitivity of as-prepared nanothermometers is optimized through modulating the Tm3+ surrounding environment and a maximum sensitivity of about 2.13% K−1 is achieved in the physiological temperature range. Besides, a parameter named as thermally coupled degree is defined in this work to quantify the coupling between the thermally coupled levels. According to the conclusion of our work, special attention has to be taken for rationally constructing FIR-based optical temperature sensors.