In an internet of things (IoT) system using an energy harvesting device and a secondary (2nd) battery, regardless of the age of the 2nd battery, the power management shortens the lifespan of the entire system. In this paper, we propose a scheme that extends the lifetime of the energy harvesting-based IoT system equipped with a Lithium 2nd battery. The proposed scheme includes several policies of using a supercapacitor as a primary energy storage, limiting the charging level according to the predicted harvesting energy, swinging the energy level around the minimum stress state of charge (SOC) level, and delaying the charge start time. Experiments with natural solar energy measurements based on a battery aging approximation model show that the proposed method can extend the operation lifetime of an existing IoT system from less than one and a half year to more than four years.