The earthwork quantity in the land of a port area has a great influence on the economy of the project. In each link of the whole life cycle of the port area project, therefore, the urgent task is to find out an accurate method for calculating the site earthwork quantity in port area and optimizing the longitudinal design. Based on the calculation principles and application status of traditional methods, the problems in earthwork calculation in the port area by using the existing methods are analyzed. The principle and operation processes of Civil 3D in the earthwork calculation are studied by drawing lessons from the Building Information Modeling (BIM). By relying on the scheme for leveling site in the petrochemical warehouse area in a port area and taking the calculation results of the traditional computing software HTCAD as a reference, the convenience and reliability of Civil 3D in the calculation of engineering quantity in the port area are tested and verified. The results show that the computational accuracy of Civil 3D is 7%~20% higher than that of HTCAD; the computational speed of Civil 3D is tens of times as much as that of HTCAD; and the modification process is even 100 times faster. This study provides theoretical and technical base for using Civil 3D to calculate the earthwork quantity in the land of the port area.