Generative Artificial Intelligence (GenAI) provides personalized cognitive support and collaboratively promotes higher-order cognitive activities with learners, offering new ideas for cultivating learners’ higher-order thinking. To deeply understand this collaborative process, this paper firstly started from the cognitive characteristics and development conditions of high-order thinking, proposed the mechanism of human-machine collaborative high-order thinking development supported by GenAI, and focused on analyzing the core mechanism of high-order thinking. Subsequently, taking this core mechanism as the theoretical foundation, the paper introduced problem-based learning as the teaching organization framework, and constructed the human-machine collaborative high-order thinking cultivation model supported by GenAI. Finally, this model was applied to the teaching practice of junior high school information technology courses. Through process-based data analysis and result-based data analysis, it was found that this model can promote students’ task progression and sustained engagement during the learning process, effectively enhancing students’ higher-order thinking. Particularly notable teaching efficacy were observed in cultivating students’ critical thinking, creative thinking, problem-solving ability and work performance. The study conducted the research on human-machine collaborative high-thinking cultivation supported by GenAI from both theoretical and practical levels, can provide new ideas for the cultivation of students’ high-order thinking and promote the effective integration of GenAI into education and teaching.