The traditional weapon target allocation method focuses on the process of weapon fire on the target, and gives insufficient consideration to the process of intelligence reconnaissance, command and control, and information transfer during the combat process. In this paper, the process of intelligence reconnaissance, command and control, and information transfer in the kill chain is integrated into the traditional weapon target allocation method, and a weapon target allocation method based on the kill chain is proposed. The method searches and corrects the damage probability matrix through the kill chain and combines with the Gurobi solver to realize more accurate weapon target allocation. The experiments use simulated data to verify the effectiveness of the method, and the results show that the Johnson-KC algorithm proposed in this paper significantly outperforms the traditional DFS and BFS algorithms in terms of kill chain search efficiency, and compared with the traditional weapon target allocation method, the kill chain-based weapon target allocation method reduces the target threat degree by nearly two times and streamlines the number of residual edges of the kill net by nearly five times.