In order to guide a flying object which uses a seeker(SKR) and an inertial navigation system(INS) properly, we should confirm that axes of both equipments are aligned in the scope expected. In this paper we have proposed a method to measure the misaligned angle between a SKR and an INS during the system integration procedure. And we expanded this method to measure misalignments between several SKRs and an INS in case of captive flight test.