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