Depressive disorder has been known to be associated with high variability in resting-state electroencephalography (EEG) signals. However, this phenomenon is often ignored in stimulus-related brain activities. This study proposed a new method to explore the EEG variability evoked by transcranial magnetic stimulation (TMS, TMS-EEG) in depressive disorder (DE) patients. The TMS-EEG data were collected from 34 DE patients and 36 healthy controls (HC). The maximum eigenvalue of the real binary correlation matrix, calculated between different trials using cross-correlation and surrogate methods, was extracted to assess trial-by-trial variability (TTV) of TMS-EEG. The new method was found to more sensitive and reliable than the standard deviation method. DE patients exhibited significantly smaller TTV in Gamma band and greater TTV in Delta band than HC. Furthermore, the HAMD-17 scores were negatively correlated with TTV values in Gamma band. This study represented the first investigation into the TTV in TMS-EEG data and revealed abnormal values in DE patients. Those findings enhance our understanding of TMS-EEG technology and provide valuable insights for studying the characteristics of DE.