CO 2 mineralization by colloidal nanoclusters of MgO or CaO represents one effective way to reduce its levels in the atmosphere. However, a high temperature (>200 °C) is required for this process. Herein, we found that the Mg 2+ -mediated Thermotoga maritima ferritin (TmFtn) nanocage has the ability to convert CO 2 (3.128 mmol per gram of protein) into MgCO 3 nanoparticles in an aqueous solution with Mg 2+ as starting materials at room temperature, but the rate of such bioconversion is relatively slow. To improve the CO 2 conversion efficiency, we constructed a two-compartment system based on threedimensional (3D) protein crystalline frameworks by using dimeric TmFtn as building blocks, which consists of two types of compartments, namely, small ferritin cavity and large interglobular space. By using the system, directed compartmentalization of Mg 2+ and carbonic anhydrase (CA) according to their difference in size can be realized using a one-pot method. Consequently, the CO 2 conversion value of the CA-encapsulated protein crystalline frameworks reaches as high as around 8.485 mmol per gram of protein, while the conversion rate increases by 2 to 3 times. Notably, its reversible disassembly and reassembly property endows the frameworks with satisfied recyclability, allowing them to be suitable for practical applications.