NIR-II fluorescent nanoprobes based on inorganic materials, including rare-earth-doped nanoparticles, single-walled carbon nanotubes, CdS quantum dots (QDs), gold nanoclusters, etc., have gained growing interest in bioimaging applications. However, these nanoprobes are usually not biodegradable and lack therapeutic functions. Herein, we developed novel NIR-II fluorescence (FL) imaging and therapeutic nanoprobes based on black phosphorus QDs (BPQDs), which exhibited excellent biodegradability and high tunability of size-dependent optical properties. By adjusting the size of nanoparticles, BPQDs can specifically accumulate in the kidney or liver. Importantly, a low dosage of BPQDs can effectively protect tissues from reactive oxygen species (ROS)-mediated damage in acute kidney and liver injury, which was real-time monitored by responsive NIR-II fluorescence imaging. Overall, we developed novel NIR-II emitting and therapeutic BPQDs with excellent biodegradability vivo, providing a promising candidate for NIR-II FL imaging and ROS scavenging.