In this paper, BaY 2 O 4 :Yb 3+ /Er 3+ , a high efficient red upconversion (UC) material, is first utilized as an optical thermometer in the biological window, accomplished through the fluorescence intensity ratio (FIR) of thermally coupled Stark sublevels of 4 F 9/2 (FIR (654/663) ). The maximum absolute sensitivity of FIR (654/663) ) is 0.19% K −1 at 298 K, which is much higher than most previous reports about FIR-based temperature sensors located in the biological windows. More importantly, the groove of FIR (654/663) for thermometry is nicely located in the physiological temperature range, indicating its potential thermometry application value in biomedicine. Furthermore, a simply ex vivo experiment is implemented to evaluate the penetration depth of the red emission in biological tissues, revealing that a detection depth of 6 mm can be achieved without any effect on the FIR values of I 654 to I 663 . Beyond that, the temperature sensing behaviors of the thermally coupled levels 2 H 11/2 and 4 S 3/2 (FIR (523/550) ) are also investigated in detail. In the studied temperature range, the absolute sensitivity of FIR (523/550) monotonously increases with the rising temperature and reaches its maximum value 0.31% K −1 at 573 K. All the results imply that BaY 2 O 4 :Yb 3+ /Er 3+ is a promising candidate for deep-tissue optical thermometry with high sensitivity.