In order to solve the calibration problem of Automatic Test Equipment (ATE), three system-level calibration methods are proposed in this paper, including grading calibration method, internal with external combinative calibration method and external comprehensive calibration method. Through comparison of advantages and disadvantages between the above-mentioned calibration methods, the applicable using range of them are proposed. The grading calibration method is applicable to testing the ATE of rich resources; Internal with external combinative calibration method and external comprehensive calibration method are applicable to all types of ATE for aviation. Considering the level of domestic development of ATE for aviation, the internal with external combinative calibration method will be used; Along with the level of the ATE development raising, external comprehensive calibration method will be the mainstream of ATE system for aviation in the future.