Air defense is a basic operational pattern of large surface warship formation. The PEPA (Performance Evaluation Process Algebra) method was applied to model the whole-process air defense operation of surface warship formation. The main air defense process, such as early warning, information transmission, giving orders and interception, was described formally. The established model which has the hierarchical structure takes into account the cooperation among elements and represents the concurrency and distributed character of the air defense operation. By doing performance index choosing and steady state analysis, it obtains the influences of different factors on the performance of air defense of warship formation. The appropriate composition of the basic formation elements in air defense operation is also obtained. Therefore, it provides a new method to deal with the air defense problem of warship formation.