Collaborative innovation in interdisciplinary teams is a collaborative approach to accomplish cooperative tasks and achieve innovative goals through a multidisciplinary intersection in the form of member combinations. The purpose of this study was to reveal the neural mechanisms underlying the impact of interdisciplinary collaboration on groups and individuals. Each group of subjects consisted of two people with and without a design background, who were asked to solve two realistic presented problems (RPP), and two design innovation tasks based on RPP adaptations. The study used hyperscanning of functional near-infrared spectroscopic (fNIRS) brain functional imaging techniques to simultaneously record the neural responses of interacting participants in each group. The study compared the innovation performance of interdisciplinary teams with design backgrounds in domain-specific versus domain-general innovation tasks, and the results showed differences in individual and group performance in different types of innovation tasks, with individual fluency being the most significant. The study may provide empirical evidence for the performance benefits of interdisciplinary teams in real-world collaborative co-innovation.