Aiming at the problems of serious cross influence， control difficulty and poor transient performance of the two output branches of the single inductor dual output Buck-Boost converter （SIDO Buck-Boost） with non-minimum phase characteristics， a control strategy based on the extended state observer （ESO） combined with the differential flatness based control （DFBC） of the main circuit and the improved dual closed-loop active disturbance rejection controller （ADRC） of the branch circuit is proposed. Firstly， based on the theory of differential flatness， a differential flatness controller is designed in the main circuit control， and error feedback is provided for the differential flatness system. ESO is designed to observe the disturbance term of the main circuit， and the observed state variables are fed back to the differential flatness controller. Secondly， to solve the problem of branch coupling and right half plane zero， an improved dual closed-loop ADRC is designed to decouple the system. The current inner loop selects ADRC based on model compensation and feedforward compensation， and the voltage outer loop selects ordinary ADRC. Then， Lyapunov theory is used to prove the stability of the system. Finally， a simulation model was built on the Matlab/Simulink platform， and an experimental platform was built based on HIL. The simulation and experimental results show that the proposed control strategy reduces the cross influence between the two output branches， solves the problem of non-minimum phase system control difficulty， and improves the transient response performance of the system.