Energy storage system play a crucial role in safeguarding the reliability and steady voltage supply within microgrids. While batteries are the prevalent choice for energy storage in such applications, their limitation in handling high‐frequency discharging and charging necessitates the incorporation of high‐energy density and high‐power density storage devices to enhance power quality, maintain power balance, and reduce fluctuations. In this study, we introduce a hybrid energy storage system (HESS) solution, combining a battery and a supercapacitor, to address intermittent power supply challenges. The effective management of this HESS is pivotal for constant DC voltage and sustaining microgrid stability. To achieve this, we propose an innovative control strategy called the Adaptive Filter‐Based Method (AFBM) for DC microgrid operation, which prioritizes stable and smooth performance while addressing safety and degradation concerns related to the storage devices. Our control strategy determines the distribution of charging and discharging currents for each storage device within the DC microgrid based on their state of charge. We conducted simulations in MATLAB/Simulink, comparing the proposed AFBM method with the conventional filter‐based approach using identical configurations, parameters, and operational modes. The results demonstrate the superior performance of our proposed system, showcasing improved voltage stability, more equitable load distribution, and efficient charging and discharging of storage devices compared to the traditional method. This research contributes to the advancement of microgrid energy storage solutions, enhancing their reliability and performance.