In view of the fact that the high altitude wind, a random factor, often leads to poor robustness of the longitudinal separation between two aircraft in the longitudinal autonomous separation maintenance problem under the random disturbance of track, this paper proposed a longitudinal autonomous separation control method based on model predictive control (MPC). Firstly, the linear time-varying prediction model was developed by establishing the nonlinear kinematics differential equation of the longitudinal separation and the wind field difference between the two aircraft. The longitudinal separation and route deviation distance of the two aircraft was selected as the optimization objectives, the vacuum speed and yaw angle of the front aircraft were taken as the measurable disturbances, and the high-altitude wind was the random disturbance. Terminal equality constraints were added to the air safety and aircraft performance constraints to maintain the stability of the system. To verify the effectiveness of the proposed method, within the specified 120-second simulation time, this article set three sets of different expected separations of 12 km, 13 km, and 14 km. Through the design of an MPC controller, the vacuum speed and yaw angle of the following aircraft were controlled during the rolling time domain cycle. The separation curve between the two aircraft is relatively smooth and always not less than the minimum safety separation of 10 km. It stabilized at the expected target separation in the 74th second, 90th second, and 118th second, and returned to the route starting from the 58th second, 74th second, and 95th second. Two sets of wind field control groups were set up. Two times as much wind was forecast in one group, while eight times as much turbulent wind was disturbed in the other. Both groups were able to establish the expected interval of 12 km smoothly and stably in the 61th second and 72th second, respectively.