In view of the needs of the engineering education certification for the building environment and energy engineering in the new era, the top-level design of the course syllabus was carried out on the basis of understanding the engineering education certification system and the course of fundamentals and equipment of heat-mass transfer was taken as an example. The course syllabus design method and writing idea were expounded in detail from the aspects of course information, course introduction, course objectives, the corresponding relationship between course objectives and graduation requirements and its index points, course main content and the allocation of class hours, course teaching methods, course assessment and evaluation methods, and course recommendation materials. The application verification of engineering education certification in Lanzhou Jiaotong University in 2021 shows that the course syllabus design method meets the requirements of engineering education certification, and the course teaching method and course evaluation are reasonable, which is conducive to the evaluation of the achievement of course objectives. This study can provide reference for the revision of the curriculum of engineering education certification.