Understanding social interaction from various human behaviors is a complex task. Hyperscanning research tackles this challenge by delving into behavioral mechanisms through a neuroscience lens. While traditional studies focus on inter-brain synchrony in paired functional brain networks, they often lack methods for measuring interactions at the group level. In this study, we propose a multilayer network approach to estimate group brain synchrony and gain deeper insights into the brain’s intricate organization. By utilizing the Prisoner’s Dilemma Game, our goal is to find group interaction processes through distinct behaviors such as cooperation and defection. Thus, the inter-brain synchrony along with differences in network connectivity and structural properties within the functional group network were statistically analyzed between cooperation and defection.