To address the difficulty of obtaining real time-delay signals due to the channel fading caused by multipath effect for acoustic signals in shallow waters，an ultra-short baseline(USBL)device is developed for shallow-water positioning，and a cross-correlation time-delay estimation method with constraints is proposed. Pulse selection and phase correction method for time-delay difference are used to accurately track and locate the target trajectory. The results of a lake experiment show that the positioning trajectory of the proposed method is smooth and stable，with few wild points and high positioning accuracy.