Acute organ injuries, such as acute kidney injury (AKI) and acute liver injury (ALI), usually present high morbidity and mortality in patients. However, the current clinical treatments remain limited, especially the lack of effective drug‐based treatment. Since these acute injuries are often associated with reactive oxygen species (ROS) overproduction, it is a promising strategy to develop therapeutic agents with potent ROS scavenging ability and excellent biocompatibility for efficient antioxidation therapy. Black phosphorus quantum dots (BPQDs), low‐dimensional nanomaterials prepared through a straightforward one‐step method and capable of complete controllable biodegradation, offer significant potential. This study comprehensively explores the extensive free‐radical scavenging capabilities of BPQDs, underscoring their immense potential in treating ROS‐related organ injuries. BPQDs could simultaneously achieve radical scavenging of DPPH, ABTS·, OH·, and O2−· and exhibit excellent cytoprotective effects against ROS‐mediated damage even at extremely low dosages. Besides, the ultrasmall size of BPQDs (≈3‐5 nm) allows them to effectively penetrate the glomerular filtration barrier (≈6 nm), significantly improving the symptoms of AKI and ALI in vivo. The therapeutic efficacy and great biocompatibility of BPQDs facilitate the clinical management of ROS‐related diseases, which will broaden the applications of QDs in the field of biomedicine.