Due to the distinctive aerodynamic designs which is different from the conventional ones, flying-wing aircraft are characterized by stronger coupling among the three channels and worse attitude static stability. Therefore, this paper proposed a decoupling control algorithm on the basic of linear extended state observer (LESO). Initially, a six-degree-of-freedom model of a flying-wing aircraft was established. Subsequently, LESOs were designed respectively for the channel of angle of attack, sideslip angle and roll angle. The aggregated disturbance, which includes the coupling terms among the channels, was estimated and compensated by LESOs, thereby achieving control decoupling. Once decoupling is achieved, linear controllers were designed respectively for each channel, and the stability of the entire dynamic system under control was proved according to the Lyapunov stability criterion. The simulation results demonstrate that the designed decoupling control method effectively suppresses static errors caused by coupling terms, and simultaneously enhancing the performance of the control system.