In inquiry-based learning, curiosity is the key factor driving students to actively explore and engage in deep learning, while the cultivation of higher-order thinking skills is a core objective. However, some students may lose interest and motivation due to difficulties or uncertainties encountered during the learning process, which can negatively impact learning outcomes and limit the full benefits of inquiry-based learning. Therefore, providing timely and adaptive prompts has become an essential strategy for enhancing learning engagement and cognitive development. This study developed an Auto-Prompt Learning Aid (APLA), which dynamically adjusts prompt content based on students’ learning states and behavioral patterns to provide targeted learning support. The results indicate that APLA significantly enhances students’ curiosity across three dimensions: joyful exploration, sensitivity to gaps, and tolerance for uncertainty. Additionally, it effectively strengthens both cognitive and emotional engagement, encouraging students to immerse themselves more deeply in learning. Moreover, APLA contributes to the development of students’ higher-order thinking skills, particularly in problem-solving and critical thinking, demonstrating that adaptive prompts can reinforce students’ inquiry abilities and cognitive growth. The findings of this study validate the application value of APLA in inquiry-based learning and suggest that adaptive prompt systems help maximize the benefits of inquiry-based learning, fostering the development of higher-order thinking skills while optimizing students’ learning experiences and cognitive growth.