In order to explore a more applicable target allocation method for anti-missile operation， the connotation of target allocation model in multi-layer anti-missile cooperative operation is defined， and the basic idea of constructing the target allocation model of multi-layer anti-missile cooperative operation is clarified. The index system of ballistic missile threat assessment， and feasibility analysis of combat unit interception are established respectively. The ballistic missile threat assessment model and the strength analysis model of combat unit interception are established through normalization and weight assignment. On this basis， combined with the actual requirements of multi-layer and anti-missile cooperative combat firepower application， the Hungarian algorithm is improved based on vitality transfer， the target allocation model of multi-layer anti-missile cooperative operation based on improved Hungarian algorithm is constructed. And the model is used to simulate the case with the background of multi-layer anti-missile combat scenario to verify the rationality and effectiveness of the model.