In recent years, the life cycle of industrial products becomes shorter and shorter; the diversity and complexity of functionality are continuously increasing. Thus, conventional methods and techniques of industrial controller design can no longer satisfy the actual demands like smartness, miniaturization, short time-to-market, etc. This paper is devoted to elaborate a methodology for hybrid controller design and high-level synthesis, combining discrete event system (DES) and continuous time system (CTS). This methodology includes successive system analysis, DES specification, GRAFCET modeling, DES/CTS interfacing, VHDL-based synthesis and FPGA hardware realization. We took a drilling machine as an example to apply this structural and automatic design procedure and achieved high-level hardware synthesis. This example demonstrates integrated design and rapid prototyping of our methodology which are valuable for industries.