This paper addresses the issue of bus voltage fluctuations caused by uncertain factors， such as power fluctuations in distributed photovoltaic systems and frequent switching of loads in direct current （DC） microgrids. The study focuses on a three-phase interleaved parallel bidirectional DC-DC converter in the energy storage unit of the microgrid and proposes a differential flatness-based and improved super-twisting sliding mode dual closed-loop composite control strategy based on a cascade finite-time extended state observer （CFT-ESO）. Firstly， a mathematical model of the three-phase interleaved parallel bidirectional DC-DC converter is established. The DC system is transformed into a differentially flat system based on the theory of differential flatness. The estimation accuracy of the system’s total disturbance is improved by combining a two-level finite-time extended state observer with fast convergence. Secondly， a dual closed-loop control system is employed， with inner-loop differential flatness control and outer-loop improved super-twisting sliding mode control. This control strategy not only enhances the dynamic response of the system but also suppresses chattering using a higher-order sliding mode control algorithm， while addressing the non-minimum phase problem in the boost mode of the converter. Next， the stability of the control system is proven using Lyapunov theory. Finally， the control strategy is validated through simulations using MATLAB/Simulink software and an experimental platform. The results demonstrate that the proposed control approach effectively mitigates disturbances and improves the transient performance of the system.