A double-closed-loop linear self-resistant control strategy is designed to solve the problem of the three-phase staggered-parallel bi-directional DC-DC converter affected by uncertainty perturbations in the DC microgrid systems. Firstly, a bidirectional DC-DC mathematical model is established, and the transfer function of the converter is derived by small-signal analysis. Secondly, a double closed-loop system with second-order LADRC in the current loop and first-order LADRC in the voltage loop is designed to estimate and compensate for the external disturbances and the internal uncertainties of the system in real time by designing its corresponding linear extended state observers and linear state error feedback. Finally, the stability of the control system is proved according to the Lienard-Chipard stability criterion, and the three control strategies are simulated in MATLAB/Simulink for comparison and verification under different operating conditions. The simulation results show that, compared with the traditional proportional-integral controller, the control strategy proposed optimizes the maximum dynamic deviation ratio of the bus voltage by 0.5% and 0.97% and shortens the regulation time by 78.3% and 76.9% under the disturbances of 20% voltage increase and decrease on the energy storage side, and optimizes the maximum dynamic deviation ratio of bus voltage by 0.79% and 1.5% and shortens the regulation time by 72% under the disturbances of 20% load increase and decrease, which effectively improves the dynamic performance and anti-disturbance capability of the system under the premise of ensuring the equal flow of each phase.