Aberrant reactive oxygen species (ROS) generation is one of the crucial mediators in the pathogenesis of inflammation. So, the development of nanocatalytic medicine to catalyze the ROS-scavenging reactions in pathological regions are promising for anti-inflammatory therapy. Herein, a type of biocompatible metal free carbon dots is prepared via a hydrothermal method which can exhibit peroxidase (POD)-like, catalase (CAT)-like and superoxide dismutase (SOD)-like activities. It has been found that the carbon dots have the capability to efficiently deplete the excessive ROS such as peroxide (HO) superoxide anion (O) and hydroxyl radical (OH) for their abundant functional groups. After the tail injection in mice with liver inflammation induced by lipopolysaccharide, the carbon dots efficiently reduced the excessive production of ROS and proinflammatory cytokines in vitro. Both in vitro and in vivo results endowed the biocompatible carbon dots with great potential in nanocatalytic medicine for the treatment of disease.