In order to absorb the regenerative power and to reduce the peak input power of a train-in other words, to smooth the input power of the train-in this paper we repot a frequency-domain-based power controlling strategy for energy storage of hybrid electric railway vehicles. Applying a loss-compensating method by using a disturbance observer improves the energy while keeping ability of this controller. However, that loss compensating method requires precise voltage-energy characteristics of the supercapacitor (SC) to estimate the correct loss. Hence, nonlinearity of the capacitance of the SC becomes a problem because it causes an error in the estimated loss. Therefore, this paper presents a method to measure the voltage-energy characteristics precisely of the SC that has a voltage dependence on the capacitance. A method to implement those characteristics into controllers is also proposed. The loss compensating method is applied to a controller by using the proposed method, and its effectiveness is verified by a small-scale experimental system.