Inflammatory bowel disease (IBD) is a chronic inflammation of the colon that is becoming increasingly prevalent. As a result, there is a growing demand for safe, effective, and non-addictive drugs. Herein, we are inspired by using carbon dots-based nanomedicines to regulate redox balance and alleviate inflammatory diseases. Specifically, histidine-derived carbon dots (His-CDs) with antioxidant and multi-enzyme (superoxide dismutase, catalase) activities are synthesized, which not only improve intestinal redox balance, but also demonstrate promising potential in modulating gut microbiota for the treatment of IBD. To understand that underlying activities mechanisms of His-CDs, their precursors, structures, and band gaps are carefully analyzed. Our investigations show that His-CDs effectively reduce oxidative damage to cells and nematodes by scavenging free radicals. Furthermore, we confirm the anti-IBD effects of His-CDs at both cellular and mouse levels. Importantly, our research reveal that His-CDs restore intestinal homeostasis in colitis by regulating the gut microbiota. We further validate this finding through fecal microbiota transplantation, which demonstrate an increase in the abundance of beneficial bacteria in the intestinal tract following the administration of His-CDs. This investigation not only expands the knowledge of nanozymes, but also offers a promising nanomedicine approach for IBD therapy.