The best transition area of air defense missiles in layered defense system was studied aimed at problem of superposition of operation areas. Under the background of air defense operation and aimed at the problem above, established best transition area model for long-range, middle-range and short-range missiles in layered defense system on the basis of allowed number of shooting model and considering the single missile kill probability. Finally the model rationality was verified through three simulation examples. The results showed that this model can increase shooting number to targets, improve whole operational effectiveness of system, and provide reference for operational effectiveness evaluation of layered defense system and performance parameters determination of each layer of air defense missile.