Patients with β-thalassemia are prone to complications such as cardiovascular diseases and secretory gland injury due to iron overload (IO) and reactive oxygen species (ROS) production caused by blood transfusions. Simultaneously scavenging ROS and eliminating IO using nanomedicine remains challenging. Herein, we designed a dual-functional Ce-based metal–organic framework@polydopamine (Ce-MOF@PDA) composite that integrates oxidative stress reduction and IO elimination and evaluated its protective effect on IO injury in thalassemia. Using Ce-MOF with multiple active sites as the core, dopamine, which can coordinate iron ions, was modified on the surface of Ce-MOF and spontaneously polymerized to obtain PDA with iron elimination ability. Dopamine modification also adjusted the Ce³⁺/Ce⁴⁺ ratio to further enhance the catalytic activity for scavenging ROS. Ce-MOF@PDA exhibited multiple nanozyme activities, such as superoxide dismutase- and catalase-like activities, and decreased iron-mediated oxidative stress levels in vitro. Furthermore, the serum ferritin levels and iron concentrations in the liver of IO mice were reduced following treatment with Ce-MOF@PDA, and the fecal clearance ability was comparable to that of deferoxamine. These results indicate that Ce-MOF@PDA can eliminate IO while scavenging ROS and reduce tissue damage caused by oxidative stress. Therefore, the Ce-MOF@PDA nanozyme is a promising therapeutic nanomedicine for treating thalassemia IO.