The invention discloses a Ka waveband optical phase equalization system and a running method thereof. A light source, an electro-optical modulation unit, an adjustable delay unit and a photoelectric demodulation unit of the system form an optical link, and output a Ka microwave signal of equalized phase. The electro-optical modulation unit is a quadrature bias MZM modulator, the photoelectric demodulation unit is a PIN photoelectric detector, the adjustable delay unit is an optical delay module with a tuning stepping motor, a microcontroller is connected with a bias control unit and a tuning control unit and respectively controls a bias voltage of the MZM modulator and a revolving speed and a position of the tuning stepping motor, and the microcontroller is connected with an upper computer through a CAN bus. The running method is that power-on self test is carried out, and the microcontroller controls the adjustable delay unit according to a command of the upper computer to realize phase delay; and periodical self test is carried out for guaranteeing output to be normal. Optical delay is expanded to a Ka waveband, delay accuracy is up to 0.1 picosecond, and the optical delay is highly accurate, continuous and adjustable; a single host computer can perform remote control for a plurality of devices, and thus, the system is small in volume, low in power consumption, light in weight and easy to operate.