A35kV side compound voltage blocking over-current protection operation failure accident occurred on main transformer in a110kV substation. According to the on-site survey and analysis，the cause of the accident is that backup-protection did not act because the bus residual voltage was higher than the low-voltage element setting value of backup-protection of the transformer when three-phase short circuit fault occurred in distant end of35kV line. It points out that the device voltage sensitivity of transformer backup-protection on middle and low voltage side is not enough when the three-phase short circuit occurred in distant end of lines. In order to prevent occurrence of similar accidents，a countermeasure is put forward. That means to add a segment over-current protection without voltage blocking to the transformer backup-protection. The quantitative analysis is used to show the improvement of the transformer backup-protection.