In recent years, with the rapid development of integrated circuits and the widespread application of smart chips, the internal structure of complex electronic systems have become increasingly complex, which greatly increases the difficulty of board-level circuit testing and fault diagnosis of complex electronic systems. At present, traditional manual testing methods are no longer able to meet the maintenance requirements of modern complex electronic system board-level circuit. Therefore, the development of intelligent and universal automatic testing systems has become an important issue in fault detection of complex electronic systems. Based on the testing requirements of the automatic test system(ATS), this paper designs the corresponding overall scheme, software scheme and hardware circuit, and studies the fault diagnosis and test of board-level circuit of complex electronic system, and proposes to apply the traditional Bode diagram to the engineering practice of ATS. Fault detection is realized by utilizing the frequency domain characteristics of the object under test.