Based on the concept of new engineering construction, this paper explores the teaching reform of the Food Microbiology course aiming at the particularity of the demand for microbiology knowledge in the grain and oil food industry. By analyzing the existing problems in current teaching and combining the training goals of talents with grain and oil characteristics, a “theory-practice-innovation” trinity teaching reform model is proposed. In terms of teaching content, it highlights characteristic content such as grain and oil microbial detection, fermentation, and safety; in terms of teaching methods, it adopts diversified means such as online-offline blended teaching, virtual simulation experiments, and project-based learning; in terms of the evaluation system, it establishes a mechanism combining process evaluation and summative evaluation. Practice shows that this teaching model has effectively improved students’ professional literacy and practical ability, providing an effective path for cultivating high-quality applied talents adapting to the development of the grain and oil industry.