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Inquiry skills are essential in science education, especially for preparing elementary students to navigate complex information today. Online inquiry-based learning (OIBL) supports the development of such skills, but its effectiveness is often limited by weak metacognitive abilities. To address this, we designed a metacognitive scaffolding-supported OIBL (MS-OIBL) approach. A quasi-experimental study involved 165 fifth-grade students in Beijing, with 83 in the MS-OIBL group and 82 in the control group. Survey and log data showed the MS-OIBL approach significantly improved science achievement, metacognitive abilities including conditional knowledge, regulation, planning, monitoring, and evaluation, and inquiry skills, without increasing cognitive load. The findings underscore the value of embedding diverse metacognitive scaffoldings across the OIBL cycle and offer guidance for improving online science learning.