Recent years have seen significant advances in supercapacitor-based applications in portable electronics, where the switching resistor circuit acts as a common cell balancing circuit when charging the supercapacitors. However, existing charging control methods suffer from low energy efficiency, leading to considerable energy loss, and thermal heating. In this paper, we propose a state-of-health (SoH)-aware energy-efficient charging method to maximize the energy efficiency of supercapacitors during the charging process. First, we provide a sufficient and necessary condition to maximize the energy efficiency. Then, an online SoH estimation algorithm is designed to estimate capacitance and balancing resistance in real time. Thereafter, an SoH-aware energy-efficient charging algorithm is further proposed to be implemented in microcontrollers. A charger prototype has been built to verify the effectiveness of the proposed charging algorithm. Extensive simulation and experiment results show that the energy efficiency of the proposed design is improved considerably when compared with existing methods.