•A novel control method is proposed for NF, QPR and LPF based on dual-loop control.•This method improves the suppression effect of secondary harmonic current (SHC).•This method also improves anti-load mutation ability.•SHC suppression effect and dynamic response of four control methods are analyzed. The instantaneous output power of the energy storage system pulsates at twice the output voltage frequency, generating a large amount of secondary harmonic current (SHC) in the switching tubes and batteries. The SHC is harmful to the system performance and battery life. Firstly, through the analysis of traditional dual-loop (DL) control method, it is concluded that SHC is not suppressed obviously and the dynamic characteristics of the system is inferior when load hopping. To address these two questions, a novel control method is proposed for introducing notch filter (NF), quasi-proportional resonator (QPR) and load power feedforward (LPF) based on DL control (it can be abbreviated as NQLDL). This method increases the amplitude of the inductor branch equivalent impedance (IBEI) at twice the output frequency without changing the frequency adaptability, improves the suppression effect of SHC, reduces the amplitude of the IBEI outside of twice the output frequency and also improves anti-load mutation ability. Furthermore, the SHC suppression effect and dynamic response are also discussed under four control methods. Finally, the validity of proposed control methods are demonstrated by experimental results.