Against the backdrop of emerging engineering construction and professional accreditation for engineering education, the conventional teaching paradigm of Food Microbiology fails to satisfy the demand for interdisciplinary, versatile talents. Rooted in the Outcome-Based Education (OBE) philosophy, this paper conducts a comprehensive exploration into the instructional reform of Food Microbiology with distinctive grain and oil disciplinary characteristics. To start with, this paper sorts out a three-dimensional curriculum objective system covering knowledge mastery, practical competence and all-round literacy in light of corporate operational demands and disciplinary development requirements. Secondly, it systematically dismantles the whole curriculum framework and embeds curriculum-based ideological and political elements into every teaching segment. Thirdly, a hybrid online-offline teaching framework is established, supplemented by diversified instructional tactics including virtual simulation and case-based learning. Finally, an assessment mechanism integrating formative evaluation and summative evaluation is constructed, forming a closed-loop system for the continuous optimization of teaching quality. Practical outcomes demonstrate that the aforesaid teaching framework can boost students’ initiative in autonomous learning, deepen their comprehension of disciplinary knowledge, upgrade their hands-on operational capacity and optimize the overall curriculum evaluation effect, thereby offering an instructional scheme for cultivating high-caliber talents adaptive to the rapid evolution of the food industry.