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This study proposes a Dual-Layer Metacognitive Scaffolding (DLMS) framework, which aims to enhance learners’ self-regulated learning and interaction with Generative AI (GAI) in a hybrid intelligence environment. The framework was implemented through CoLearn.AI—a DLMS-supported pedagogical agent (DLMS-PA) powered by a large language model. Eight Year-2 university students majoring in English language education in Hong Kong participated in the study by designing lesson plans, sequentially supported by standard GAI and CoLearn.AI. Lesson plans and participant-GAI interaction logs were analyzed using expert ratings and Epistemic Network Analysis. Findings indicate that CoLearn.AI promoted more coherent collaboration and organized learning behaviors, leading to higher-quality lesson designs. This study contributes to the design of theory-informed scaffolding approaches that promote meaningful and productive learner-GAI partnerships.