Because of the particular environment of the tumor microenvironment, improving the deep penetration of drugs in tumor sites is a critical problem to improve the therapeutic effect of the tumor. The ultra-small nanoparticles can achieve deep tumor tissue penetration without modification, which shows tremendous significance in tumor therapy. In this work, the ultra-small permeable carbon dots (PCD) have been developed with near-infrared-II (NIR-II) window photothermal irradiation and good biocompatibility. These PCD showed multi-color fluorescence under visible light and photoacoustic signals under an excitation of 808 nm, guiding fluorescence and photoacoustic imaging for location and distribution in vitro and vivo. The PCD could penetrate the deep tissue in tumor spheroids and tissues. Meanwhile, the irradiated depth of the NIR-II window can provide sufficient photothermal energy with the deep penetration of PCD in tumor tissue to cause tumor ablation. Therefore, this PCD can be used as a safe, fluorescent, and photoacoustic imaging agent for guided NIR-II photothermal tumor therapy, which provides a new direction for the use of ultra-small carbon dots in anticancer therapy in the future.