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This study introduces an improved bidirectional multi-input DC–DC converter (MIPC) tailored for hybrid energy storage systems (HESS) in DC microgrid environments. Traditional batteries exhibit limited charge and discharge rates, which can impose high current stresses, thereby reducing their operational lifespan. Supercapacitors (SCs), due to their high power density, respond rapidly to sudden load variations, mitigating these limitations; however, they are unsuitable for long-term energy storage. Combining batteries with SCs in a HESS leverages their complementary properties, creating an efficient energy storage solution. The proposed MIPC links the HESS to the DC microgrid, enabling independent regulation of battery and SC power as well as efficient energy transfer among storage units. A unified control strategy was developed to manage both charging and discharging of the HESS. A model predictive control (MPC) scheme demonstrated superior DC bus voltage restoration during step changes in photovoltaic (PV) generation and load conditions, compared with conventional proportional-integral (PI) controllers. The MPC reduces current stress, prolongs battery lifespan, and improves overall system performance, ensuring rapid DC grid voltage stabilization. Simulation and experimental tests under varying PV output and load profiles confirmed enhanced DC-link voltage regulation.