In 2006, the former Ministry of Communications issued The Content and Text Format of Port Master Plan, which clarified the relevant requirements for planning drawings. The port master plan atlas is a means of visually expressing the content of port planning. Under the requirements of the new stage of “integration of multiple plans”, the atlas drawing of port master plans encounters the problems such as the lack of basic data on port waters and data conversion between software. To solve these problems, this paper proposes a data conversion method for port master plans based on the software FME. This method uses FME to accurately and non-destructively convert the port planning data traditionally carried by the software AutoCAD into the GIS format and extracts and converts the geographic data of electronic charts to make up for the missing basic data on port waters. Practical applications prove that the proposed method can meet the new requirements for the atlas drawing of port master plans.