To enhance the robustness and accuracy of the calculation, the treatment method for preconditioned characteristic boundary and preconditioned backflow boundaries are derived from the characteristics of preconditioned Euler equations. The preconditioned boundary treatment methods are obtained from the characteristic relation of preconditioned Euler equations, and in subsonic inlet and outlet boundaries, the backflow boundary treatment methods are acquired from the characteristic equations. Through numerical simulation, it is found that the backflow boundary treatment method converges more than 1.5 times faster, while the computational accuracy is similar to SIMPLE method; in the calculation of outlet with backflow, its pressure error is 68.3% lower than Fluent software. Thus the preconditioned backflow boundary treatment method has higher accuracy and better robustness, and is valuable in practical engineering calculation.