The widespread application of Generative Artificial Intelligence (Gen-AI) is transforming educational practices and driving pedagogical innovation. While cultivating higher-order thinking (HOT) represents a central educational goal, its achievement remains an ongoing challenge. Current evidence regarding the impact of Gen-AI on HOT is relatively fragmented, lacking systematic integration, particularly in the analysis of moderating variables. To address this gap, a meta-analysis approach was employed, integrating data from 29 experimental and quasi-experimental studies to quantitatively assess the overall impact of Gen-AI on learners’ HOT and to examine potential moderating factors. The analysis revealed that Gen-AI exerts a moderate positive effect on HOT, with the most significant improvement observed in problem-solving abilities, followed by critical thinking, while its effect on creativity is relatively limited. Moderation analyses further indicated that the impact of Gen-AI is significantly influenced by experimental duration and learners’ self-regulated learning (SRL) abilities: effects were strongest when interventions lasted 8–16 weeks, and learners with higher SRL capacities benefited more substantially. Based on the research findings, this study proposed that Gen-AI should be systematically integrated as a targeted instructional tool to foster HOT. Medium- to long-term interventions (8–16 weeks) are recommended to enhance learners’ problem-solving and critical thinking abilities. At the same time, effective approaches should also be explored to promote creative thinking through Gen-AI within existing pedagogical frameworks. Furthermore, individual learner differences should be accounted for by adopting dynamic and personalized scaffolding strategies to foster SRL, thereby maximizing the educational potential of Gen-AI in cultivating innovative talents.