The invention discloses a real-time monitoring method of the water depth in a port channel, comprising the following steps that: ultrasonic waves are incident into the bottom center position of the channel by an underwater sonar transmitting assembly arranged at one side of the channel in a certain inclination angle and reflected through the bottom of the channel into an underwater sonar receiving assembly arranged at the other side of the channel; the underwater sonar receiving assembly receives an ultrasonic signal and acquires channel water depth parameters according to the signal; and the channel water depth parameters are transmitted into a monitoring center. By adopting the method and the system, the normal operation of the channel can not be influenced, and the channel can work in severe environments of gale, billow, and the like; and the system has reasonable structure, simple installation, low cost and high measurement precision, is more suitable for engineering practice with narrow channel and beneficial to being popularized, generalized and applied.