C dots (CDs) have shown great potential in bioimaging and phototherapy. However, it is challenging to manipulate their fluorescent properties and therapeutic efficacy to satisfy the requirements for clinic applications. In this study, we prepared S, Se-codoped CDs via a hydrothermal method and demonstrated that the doping resulted in excitation wavelength-independent near-infrared (NIR) emissions of the CDs, with peaks at 731 and 820 nm. Significantly, the CDs exhibited a photothermal conversion efficiency of ~58.2%, which is the highest reported value for C nanostructures and is comparable to that of Au nanostructures. Moreover, the CDs had a large two-photon absorption cross section (~30, 045 GM), which allowed NIR emissions and the photothermal conversion of the CDs through the two-photon excitation (TPE) mechanism. In vitro and in vivo tests suggested that CDs can function as new multifunctional phototheranostic agents for the TPE fluorescence imaging and photothermal therapy of cancer cells.