In this paper, BaY2O4:Yb3+/Er3+, 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 F-4(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 H-2(11/2) and S-4(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 BaY2O4:Yb3+/Er3+ is a promising candidate for deep-tissue optical thermometry with high sensitivity.