There is an increasing need to evaluate environmental impacts at higher policy planning levels, especially after the European Union (EU) strategic environmental assessment (SEA) directive proposed in 2001. However, integrating SEA and policy planning processes is challenging owing to institutional challenges and/or political problems. We aimed to explore the challenges of this integration process through in-depth interviews with core stakeholders in Taiwan energy policy making. Our results reveal three main types of challenge related to policy planning, SEA implementation, and difficulties in dealing with environmental issues. The first includes the policy planning model, transparency in the policy planning process, and controversial issues clarification; the second includes the different types of SEA purposes, unclear feedback on policy planning, and public participation limitation; the third includes a lack of knowledge of brokerage processes, scientific uncertainty, the role of the Taiwan EPA (TEPA) for environmental thinking, and the influence of local information in policy planning. The results of this study can be applied to countries that use impact-oriented SEA (currently the most common type of SEA) and consider environmental issues during the energy policy planning process.