This study aims to identify the brain activation patterns of middle school students during their learning activities based on the metaverse-based ecosystem. The metaverse-based ecosystem of 13 species inhabiting coastal reefs was designed for the learning program of the experimental group, while the control group was provided with a Zoom learning program with the same content. Analyzing the average brain activity within the metaversebased ecosystem revealed predominantly left-sided brain activation in the fNIRS system. This suggests heightened activity in areas associated with visual stimuli and observational learning tasks characteristic of the metaverse. General Linear Model (GLM) analysis indicated increased activity in the left Ventrolateral Prefrontal Cortex (VLPFC) region and decreased activity in the left Dorsolateral Prefrontal Cortex (DLPFC) region, indicating engagement in interactions with objects and others during inquiry activities within the metaverse-based ecosystem. Comparative analysis with a control task showed reduced activity in the right Orbitofrontal Cortex (OFC) region related to negative emotions and in the Frontopolar (FP) region associated with goal-oriented thinking and metacognition. This suggests a shift in affective and cognitive domains compared to non-face-to-face platforms, with students exhibiting relatively positive emotions but reduced goal-oriented thinking when using the metaverse.