In non-neuroscience-based studies, economists demonstrate that humans make suboptimal economic contributions (between zero and the theoretical maximum) in collective-action scenarios. Using a neuroeconomics experiment that integrates economics and neuroscience, this study investigates why humans make such suboptimal economic contributions. In this study, 90 adult participants, divided into 15 smaller groups, collectively participated in a computer-based public goods game while wearing electroencephalography headsets that recorded their neural activities during the game. The results show that when participants modified institutional arrangements (such as face-to-face communication), their economic contributions increased, albeit suboptimally. Furthermore, simultaneously and suboptimally in the frontal and temporal lobes, the participants’ positive rationality and emotionality increased, whereas their negative rationality and emotionality decreased. We suggest that suboptimal rationality and emotionality may underlie suboptimal economic contributions. This study offers broad implications for collectively and sustainably managing local, regional, and global commons, including the atmosphere in which humans cause climate change.