Based on the fundamental concepts of the Teaching Elements Theory, this study constructs a four-level framework of key elements for graduate teaching assistants (GTAs), and systematically identifies six critical components of GTA programs: role definition, recruitment, pre-service training, stipend support, performance evaluation, and daily management. By elaborating on the logical relationships and functional positioning among these four hierarchical levels, the theoretical foundation and operational mechanisms of the GTA system are clarified. Using the practice of the GTA program at Chongqing University as a case study, the paper explores the development of an institution-specific operational model. Specific strategies for optimizing the GTA environment, refining operational mechanisms, and innovating management approaches are presented, demonstrating the system’s practical effectiveness in enhancing teaching quality, strengthening instructional support, and promoting the comprehensive development of graduate students. The findings indicate that a scientifically designed GTA element framework facilitates the standardization and efficient operation of GTA programs in higher education, offering a replicable model for the effective organization and management of instructional support staff. This research holds both theoretical value and practical significance for deepening teaching management reforms and improving the quality of graduate education.