<p>The online inquiry-based learning (OIBL) environment enhances autonomy and provides a safe context for implementing science education. It facilitates the development of students’ inquiry skills and understanding of scientific concepts. However, the effectiveness of OIBL is often compromised by students’ limited metacognitive abilities, particularly in planning, monitoring, and evaluating their inquiry processes. To address this challenge, this study designed a metacognitive scaffolding-supported online inquiry-based learning (MS-OIBL) approach to enhance students’ self-regulation and support effective inquiry learning in OIBL environments. A quasi-experimental study was conducted with fifth-grade students at two similar-level schools in Beijing, China. The study evaluated the impact of the MS-OIBL approach on students’ science achievement, metacognitive ability, and inquiry skills. Data were collected through surveys and log entries. A total of 236 students participated; 121 in the experimental group used the MS-OIBL approach, and 115 in the control group used a traditional OIBL approach without metacognitive scaffolding. The results revealed that the MS-OIBL group significantly outperformed the traditional OIBL group in terms of science achievement, metacognitive regulation ability, and inquiry skills. However, no significant differences were found between the two groups in overall metacognitive ability or metacognitive knowledge. These findings suggest that the MS-OIBL approach effectively improves students’ science performance and inquiry skills. It also promotes metacognitive regulation behavior and enhances metacognitive regulation ability. This study provides valuable insights for teachers, students, and researchers in the fields of science education and metacognition. It highlights the potential of metacognitive scaffolding to optimize online inquiry learning environments.</p>