The phase imbalance between receiving channels of a phase array antenna, referred to as phase offset, is one of the most crucial parameters in positioning the targets in lower and upper atmospheres using spatial domain interferometry (SDI) technique. In this study, we develop a method of using commercial aircraft that equips with Automatic Dependent Surveillance-Broadcast (ADS-B) system to estimate the system phase offsets of the Chungli VHF radar. The aviation data broadcasted from ADS-B system combined with the radar returns from the aircraft can obtain the system phase offset. The principle of the method and the algorithms of processing the ADS-B messages are described and the procedures of analyzing the aircraft echoes are also detailed in this article. On the basis of this method, multirotor equipped with a high precision GPS receiver is also employed to estimate radar system phase offset. The results show that the system phase offsets estimated by the aircraft and those from the multirotor are consistent. However, the aircraft/multirotor-derived system phase offsets are very different from those estimated from the radar returns of the 3-m ionospheric field-aligned plasma irregularities (FAIs) combined with International Geomagnetic Reference Field 12th generation (IGRF-12) model. The principle of the FAI method is introduced and the plausible causes of the discrepancies in the estimated system phase offsets between aircraft/multirotor and FAIs are discussed.