Carbon dots (CDs) are highly desired in biological applications. However, achieving a balance between photoluminescence (PL) efficiency and photothermal conversion efficiency (PTCE) is challenging. In this study, an unprecedent combination of efficient red fluorescence and high PTCE in the second near-infrared (NIR-II) window in a sodium-doped CDs system is reported. Upon 808 nm laser irradiation, photo-induced oxidation–reduction reactions happened on the surface of sodium cation-functionalized CDs (Na-CDs), leading to the partial reduction of surface-functionalized sodium (Na) ions. The photo-reduced Na atoms coordinated with sp C domains in the core, resulting in Na-doped CDs (ir-Na-CDs) with an enhanced absorption band in the NIR-II window and a high PTCE of 43% under 1064 nm laser irradiation (1 W cm). Composing the ir-Na-CDs with bovine serum albumin (BSA) enhanced the PLQY of the red emission to 31% in water without diminishing the PTCE in the NIR-II region. Transient absorption spectra revealed that no energy transfer occurred between the red emission center and the NIR-II absorption band, revealing a novel CDs system with independent Janus photophysical processes. Moreover, ir-Na-CDs@BSA exhibited negligible to low cytotoxicity and demonstrated tumor accumulation capacity after intravenous injection, enabling effective tumor photothermal therapy in the NIR-II region.