In this paper, the framework system of engineering management methodology has been constructed on the three levels: philosophical methodology, general methodology and specific methodology. The main methods of philosophical methodology of engineering management include seeking truth from facts, contradiction analysis, unity of knowledge and practice, unity of truth and value and dialectical thinking. The general methodology of engineering management is represented by system science, information science and mathematical methods. The main methods of the specific methodology of engineering management are composed of case study and other nine methods. This framework is not absolute as the methods of system engineering and project management are extended to all the three levels.