Aiming at the problem that the depth measurement system of under-water rock dumping construction cannot provide the real-time data processing results,we develop the automatic wave filtering function of multi-beam depth measurement data processing system with CUBE algorithm,and achieve that the quasi-real-time processing of multi-beam depth measurement data is provided,as well as the actual rock dumping section compare with design section.We apply this system in a case of deep-water breakwater construction.The results show that the system can play an assistant decision-making role in underwater rock dumping construction,and improve the efficiency and accuracy,which can provide references for the similar projects.