For the extension project of many port projects，the wave condition of the breakwater head is relatively bad and the transition and connection between old and new breakwater are complex. The design is difficult and the construction quality is more difficult to guarantee. Based on a foreign project，we optimize a design scheme with the minimum amount of removal armor blocks according to the design principle of cushion inverted filter. Combining with Civil 3D software’s function of the 3D model and 2D drawing，we propose a 3D design method to deal with the transition of various complex interfaces. The results show that the design of new and old breakwaters can be clearly and accurately completed by BIM 3D technology and an inverted filter design principle. Meanwhile，the 3D model provides an accurate and feasible reference for construction.