The rapid advancement of generative artificial intelligence (GAI) technology has had a significant impact on the field of education. In the 21st century, education places greater emphasis on fostering students’ capacities and core literacies. This research aims to examine the impact of GAI applications in teaching on students’ higher-order thinking ability. This study utilizes a meta-analysis approach to evaluate relevant domestic and international studies. Findings indicate that GAI can significantly enhance students’ higher-order thinking ability, particularly within higher education settings. This improvement encompasses critical thinking, innovative thinking, and problem-solving ability. Moreover, the research reveals that various approaches to integrating GAI into education yield differing impacts on students’ higher-order thinking ability. Through a thorough analysis and discussion of these findings, this paper offers insights and recommendations for fostering effective Student-GAI-Teacher collaboration in a man-machine learning environment.