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 4F9/2 (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 I654 to I663. Beyond that, the temperature sensing behaviors of the thermally coupled levels 2H11/2 and 4S3/2 (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.