The teledyne benthos C3D bathymetry side scan sonar system is a pioneer and innovator designed to serve marine surveys. C3D is a fully integrated sonar system that acquires high resolution side scan sonar imagery plus high resolution wide swath bathymetry to produce an accurate 3D map of the ocean floor in shallow water surveys. The C3D is a phase-differencing bathymetric sonar that uses the CAATI (Computed Angle of Arrival Transient Imaging) Algorithm to solve for multiple angles of arrival to achieve a 10 times water depth swath (for bathymetry) of high resolution (vertical 5 cm) bathymetry and imagery (horizontal 10 cm). Firstly, the basic principle, composition, performance, advantages and application of C3D System were introduced in this paper. Then, the C3D surveying system was designed and applied in artificial reef construction for the first time in China. In design, construction and monitoring phases of artificial reef, the C3D surveying system could provide high accuracy bathymetry data, high resolution submarine geomorphology imagery, depth contour, seabed grade, location and conditions of artificial reef, etc.. These information were the necessary data for artificial reef construction successfully. The tests proved the C3D is a superior performance underwater survey system which could be successfully used in various phases of artificial reef construction and guarantee the construction effect.