High-story structure design is a professional course of civil engineering majors. Combining the results of the student questionnaire survey and teaching experience of the subject group, this paper expounds and analyzes the current problems and the current situation of teaching reform of the multi-high-story structure design course. According to the characteristics of ordinary undergraduate colleges, our subject group puts forward a reform plan, named modular counterexample teaching method. Teaching content is re-modularized according to the structure type. Teaching methods are based on self-proposed counterexample teaching method and question method, and the assessment method draws on the examination mode of National Registered Structural Engineer Professional Qualification, which is output-oriented and combines the formative evaluation and comprehensive evaluation. Through the teaching reform practice in the past two years, although the academic performance needs to be further improved, the classroom effect and learning atmosphere have been substantially improved, which has verified its feasibility and good application prospects.