The engineering project cost management guided by value chain thought is helpful for enterprise to hold the key of the project and ensure the benefit. According to the characteristics of the port and waterway engineering project, the value chain thought and project cost management theory, a system method of project cost management of port and waterway engineering, which is divided into 4 stages including compiling project resource plan and classification WBS, estimating project,compiling baseline plan as well as tracking and correcting deviation,is proposed based on the value chain. The method and the key point of project cost management during each stage based on the value chain are researched and empirical analysis is carried out combining with practical engineering projects.