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The development of students’ core disciplinary competencies is crucial to the quality of talent cultivation against the background of China’s New Engineering Education initiative. We condensed a literacy–ability–knowledge model of the core competence structure of university students based on the results of a survey and then applied this model with a special focus on competence structures. We coded the core competency indicators of the course area using a software engineering course as an example to construct a map of the core competencies of the course (area). New teaching and instruction methods to promote the development of students’ core competencies were then explored. Finally, to shape core subject competence, we suggest building a course recommendation system that aligns with an employment guidance service based on the certification of core subject competence to realize a new mode of cultivating competence.