Abstract: This study proposes a high-resolution imaging method based on rubidium atomic clock to address the spatiotemporal synchronization problem in the downward looking 3D underwater acoustic imaging system. The aim is to solve the motion space limitation and electrical time delay, thereby further improving the underwater acoustic imaging quality of small targets. This method applies the principle of acoustic calibration to construct an accurate positioning model, combined with underwater time-frequency synchronization technology based on rubidium atomic clock, which can effectively solve the problem of high-precision delay error. Numerical simulation and lake experiments show that the entire system achieves nanosecond level synchronization of signal subsystems such as emission, calibration, and acquisition through high-precision atomic clock timing. By using subwavelength level acoustic calibration, 3 cm resolution small target imaging results with better reconstruction quality were obtained at an imaging distance of 30 m, providing a feasible technical path for high-resolution 3D underwater acoustic imaging of small targets at further distances.