Thallium (Tl) is an extremely toxic heavy metal and exists in very low concentrations in the environment, but its sensing is largely underexplored as compared to its neighboring elements in the periodic table (especially mercury and lead). In this work, we developed a ratiometric phosphorescent nanoprobe for thallium detection based on Mn-doped ZnSe quantum dots (QDs) and water-soluble carbon dots (C-dots). Upon excitation with 360 nm, Mn-doped ZnSe QDs and C-dots can emit long-lived and spectrally resolved phosphorescence at 580 and 440 nm, respectively. In the presence of thallium, the phosphorescence emission from Mn-doped ZnSe QDs could be selectively quenched, while that from C-dots retained unchanged. Therefore, a ratiometric phosphorescent probe was thus developed, which can eliminate the potential influence from both background fluorescence and other analyte-independent external environment factors. Several other heavy metal ions caused interferences to thallium detection but could be efficiently masked with EDTA. The proposed method offered a detection limit of 1 μg/L, which is among the most sensitive probes ever reported. Successful application of this method for thallium detection in biological serum as well as in environmental water and soil samples was demonstrated.