The trajectory of intercept hypersonic vehicle in Near Space was designed with trajectory programming method. The problem of intercepting the hypersonic vehicle in near space was analyzed and defined as long-range hypersonic intercept problem in near space, and the requirements for trajectory programming were proposed. A two-stage boost engine interceptor was designed, and the interceptor mass point model of plane motion was built in considering the earth curvature and rotation. And then, according to the requirements of trajectory programming, the trajectory restraint was designed. And the trajectory problem was established with such indexes, they were maximum terminal velocity, minimum distance error to the final point and minimum whole heat quantity. Particle swarm optimization algorithm was used to solve the problem. Results show that the programmed trajectory is a lofted trajectory which can fly out of atmosphere and reenter into it. When comparing with the proportion navigation trajectory and the near optimal trajectory, the missile will fly outside of atmospheric for most time, which can reduce the aerodynamic heat effects and cut down the requirements for the material, and provide a better initial operation environment for the terminal guidance phase.