In view of the problem of multi-missile interception of atmospheric high-speed maneuvering targets, this paper proposed a multi-missile interception decision method based on footprint prediction. Firstly, based on the maneuvering ability analysis and curve fitting method of the interceptor, the analytical model of its footprint was established, and the boundary of the footprint of the interceptor was generated with the given launch point and predicted interception point. Secondly, combined with the fast footprint prediction method of the offensive, the multi-missile interception decision-making method of the high-speed maneuvering target was transformed into the optimization problem of the coverage of the offensive and defensive footprint, and the optimization algorithm was designed to solve the multi-missile interception strategy, which used the least interceptors to cover the maximum range of the footprint of the offensive. Finally, the effectiveness of the proposed method was verified by numerical simulation.