The evolution of artificial intelligence (AI) is transforming how students acquire and apply knowledge across fields, shifting the focus of education from knowledge transmission to thinking cultivation, competency development, and the nurturing of intellectual depth. As a result, liberal education has become increasingly vital as a foundation for developing higher-order thinking. Operational thinking, a core component of liberal education, helps students engage in systematic planning, coordination, and informed decision-making in complex and uncertain environments. This paper proposes a metacognition-driven and AI-enabled methodology to enhance operational thinking within liberal education. The instructional reform is guided by principles of metacognitive instructional design, focusing on operational thinking development, and supported by generative AI technologies that provide personalized learning assistance and real-time feedback. The teaching assessment is composed of three dimensions: operational thinking knowledge, metacognitive ability, and AI cognitive ability. This paper conducts an analysis of coursework scores and satisfaction feedback from 210 undergraduate students over three semesters. The average course scores and satisfaction levels were both high, and students performed well in learning operational thinking knowledge. With the widespread development of AI technology, students’ scores in each dimension have been gradually increasing. These results suggest that the proposed model is effective and provides a useful direction for improving liberal education in the age of AI.