There has been more government commissioned studies causing a variety of problems. Agency problems are one of the problems that attract most attention. There are some shortcomings for previous studies that focused on the agency problems of government commissioned studies, such as meta- and static approach, and the lack of repeated games. Therefore, this study proposes an approach to integrating Game Theory and Agency Theory, and then uses literature review, content analysis and case study to explore the agency problems of the commissioned study of the Kaohsiung City GHG Strategy Program. On one hand, this study proposes three types of agency problems and seven agency problems; on the other hand, this study integrates Game Theory to explore the participants, rules, strategies, and payoffs of government commissioned studies. The research results show that the research approach of integrating Game theory presenting players' strategy interdependence is one of the most important causes for agency problems. The results also show that not only the integration of Game Theory can describe the agency problems better, but also addresses the strategies and actions that few studies ever addressed. Lastly, this study also proposes concrete suggestions and solutions to the agency problems of government commissioned studies.