Aimed at the high velocity and unpredictable trajectory characteristics of the hypersonic targets in near space, the optimal midcourse trajectory design and trajectory cluster generation methods were proposed for the effective coverage of the target’s predicted impact area. Firstly, by analyzing the challenges that the hypersonic targets have formed to the existing air defense systems, the necessity of the trajectory cluster design and generation in midcourse phase was illustrated. Secondly, the optimal midcourse trajectory design was treated as the problem of searching for optimal solutions under numerous constrains, and the nominal optimal trajectory was generated with the optimal control theory. Thirdly, based on the NOC (neighboring optimal control) theory, the neighboring optimal trajectory cluster generation algorithm was developed to meet the adjusted terminal constraints. Finally, the simulation results testify the effectiveness of the proposed method.