In order to correct the navigation error of midlong range airtoair missile in the inertial midcourse guidance, a method of command amendment inertial midcourse guidance is proposed by adopting a dual aircraft cooperation method. Firstly, a motion equation of midcourse guidance is established, the principle of dual aircraft cooperative detection to obtain the position information and the angle information of the missile are introduced, and a method of solving the navigation information for missile computer is given. Secondly, the system with command amendment for strapdown inertial navigation system (SINS) is designed, and a state equation and a quantity equation of the system are listed. Moreover, to solve the nonlinear problem of navigation system, the novel algorithm of Unscented Kalman Filter (UKF) is introduced. The simulation results show that the position method by dual aircraft cooperation can precisely calculate the navigation information of the missile in a certain range. The UKF algorithm is useful to solve the problem of navigation system, and the method of command amendment based on dual aircraft cooperation can correct the navigation error of SINS, and can also improve the precision of the midcourse guidance.