In order to improve the reliability of over-current/instantaneous trip protection under CT over-saturation condition and avoid protection operation-failure, this paper presents a useful analysis method of the variation trend of the measurement value of the protection along with short current. The transfer characteristic and output waveform feature as well as measurment performance of relay protection device during CT over-saturation condition are analyzed. It is shown that when fault current is several times larger than CT rated accurate limit primary current (i.e. CT is over-saturated), the characteristic value on the CT secondary side monotonously increases slowly, but the measurement value of the protection devices may decrease along with the increase of the fault current, which causes the failure of the protection. The analysis method calculates the measurement variation trend of the short-circuited current to verify the reliability of the setting values of instantaneous over-current protection, therefore, some proper measures can be taken to avoid the protection failure under this condition. It will have good economy benefits in the real applications.