Biocatalysis is playing an increasingly important role for chemical, pharmaceutical, and food industries, owing to its high efficiency, selectivity and environment‐friendliness. However, it remains challenging to improve the catalytic activity of enzymes since the most frequently used strategies are costly and time‐consuming. In the current study, a new type of glycogen‐based dynamic nano‐frameworks is prepared as additives for the direct activation of carbonic anhydrase (bovine erythrocytes [bCA]). The boronic acid functionalization of the branched glycogen structures can provide NB coordination with bCA, leading to the conjugation and stabilization of the target enzyme. As a result, the glycogen with a 10% substitution degree (Gly‐PBA10) showed a higher activation effect for bCA than that of glycogen with a 20% substitution degree (Gly‐PBA20). Furthermore, the mechanism for interactions between the dynamic frameworks and bCA has been studied through combined techniques of dynamic light scattering, circular dichroism spectroscopy, and isothermal titration calorimetry. The results suggested different protein binding modes and stabilization abilities for the protein secondary structures from these two types of functionalized dynamic frameworks. This study provided new insights into the protein‐polymer interactions that can be beneficial for various biochemical applications.