Aiming at the problem of autonomous longitudinal separation under random disturbance of flight path, the random factor of high-altitude wind often leads to poor robustness of longitudinal separation between two aircraft. This paper proposes an autonomous longitudinal separation control method for aircraft based on model predictive control. Firstly, the nonlinear kinematic differential equation of the wind field difference between the two aircraft and the longitudinal separation is established, and the linear time-varying prediction model is derived. The longitudinal separation and path deviation distance of the two aircraft are selected as the optimization objectives, the high-altitude wind is the random disturbance, and the true airspeed and yaw angle of the leading aircraft are measurable. Terminal equality constraints are added to the air safety and aircraft performance constraints to maintain the stability of the system. To verify the effectiveness of the algorithm, within the prescribed simulation time of 120 seconds, this paper sets three groups of different expected intervals 12, 13, 14km. Through the designed MPC controller, by controlling the true airspeed and yaw angle of the trailing aircraft within the rolling time domain period, the interval curve between the two aircraft is relatively smooth and is always not less than the minimum safety interval of 10 km. It stabilizes at the expected target interval at the 74th, 90th and 118th seconds respectively, and begins to return to the route at the 58th, 74th and 95th seconds, and finally returns to the center line of the route; two groups of wind field control groups are set up, one group is the forecast wind intensity increased by 2 times, and the other group is the turbulent wind disturbance intensity increased by 8 times. Both can smoothly and stably establish the expected interval of 12 km at the 61st and 72nd seconds respectively.