The paper expounds the necessity of adopting the software P3E/C in the Marine Protection Works of Pakistan Deepwater Container Port, and illustrates the functions and characteristics of it. Based on the breakwater engineering, it summarizes the preparation work for the application of software P3E/C in engineering,and expounds the application of P3E/C about progress control, cost control, quality control and HSE control. The application of P3E/C will be helpful for the establishment of the project management system which is characterized by informatization, professionalization and standardization.