Integrating ChatGPT into educational contexts has become prevalent due to its potential to revolutionize teaching, learning, and research. However, to ensure positive use, it is necessary to design learning environments that effectively incorporate this technology. This study employed self-determination theory as an undergirding framework to understand the impact of ChatGPT-integrated instruction on undergraduate students' research skills. Moreover, the study explored the impact of ChatGPT-integrated instruction on students' autonomous motivation, engagement, and self-directed learning, as well as the mediating role of these variables in the relationship between ChatGPT usage and research skills. In this quasi-experimental study, 366 undergraduate students majoring in education were divided into control and experimental groups. The control group received instruction without ChatGPT, while the experimental group received ChatGPT-integrated instruction and was allowed to use ChatGPT for research-related activities. The results revealed that the experimental group had significantly higher levels of research skills, motivation, engagement, and self-directed learning behavior. Moreover, the use of ChatGPT has a significant indirect impact on students' research skills through the mediating variables. This suggests that high autonomous motivation and self-directed learning are crucial for students to fully benefit from ChatGPT in developing research skills. The findings offer valuable insights for educators to design AI-enhanced learning environments to enhance students' research skills and learning outcomes.