The invention discloses a side-mounted draft detection system and an operating method thereof. The side-mounted draft detection system comprises high-frequency absorption modules, an ultrasonic transmitting module, an ultrasonic receiving module, pressure sensing modules, an auto-lift module, a synchronous time division control module, a data processing module and an alarm module. The high-frequency absorption modules comprise high-frequency absorbing material and fixing plates, are mounted on two sides of a navigation channel and are used for absorbing ultrasonic wave propagating to the high-frequency absorbing material, multi-path interference is eliminated, data processing is more vivid and simpler, and measuring precision is greatly improved. The synchronous time division control module controls the ultrasonic transmitting module to transmit the ultrasonic wave sequentially and cyclically at equal intervals; the ultrasonic receiving module transits effective range and strength information of received direct wave to the data processing module; draft of a ship is calculated finally; the auto-lift module can adjust underwater depths of the fixing plates provided with ultrasonic sensors, on two sides of the navigation channel, according to level change information, thereby adapting to water level changes and facilitating maintenance.