The invention discloses a system and a method for testing a phase-selecting switching-on controller in an intelligent transformer substation. The system comprises an analog quantity output unit, a merging unit, tested equipment and an oscillograph, the analog quantity output unit is used for providing analog quantity output, the merging unit is used for collecting analog quantity information and sending the same to the tested equipment, the tested equipment comprises the phase-selecting switching-on controller and an exit relay and is used for phase-selecting switching-on control and driving an exit relay contact to be on according to received data sent by the merging unit, and the oscillograph can realize wave recording and storing of analog quantity and digital quantity. The method includes that by checking and comparing wave forms recorded by the oscillograph, on time of the exit relay contact and zero crossing point time of triphase sine wave signals can be found, accuracy of phase-selecting switching-on can be acquired by calculating difference between the on time of the exit relay contact and the zero crossing point time of the triphase sine wave signals, and errors of the system can be corrected.