As government-industry-university-research collaboration gradually becomes the primary model for talent cultivation in the confidentiality major, the design of the curriculum system for this major has been influenced by various factors. Only by clearly identifying the factors that influence the curriculum system design for confidentiality major and understanding their extent of impact can more targeted optimization strategies for the curriculum system be proposed. This paper initially constructs a measurement scale for the factors influencing the curriculum system design for confidentiality major. Subsequently, a questionnaire was distributed to students and faculty of confidentiality major, related government departments, research institutions, and enterprise staff. Using structural equation modeling for data analysis, it was found that the level of student participation and faculty strength have a direct and significant impact on the curriculum system design for confidentiality major. Furthermore, the university development plan plays a mediating role in the influence of policy and financial support and industry–university–research joint training on the curriculum system design. Finally, the paper proposes strategies for optimizing the curriculum system design for confidentiality major.