Due to the internal structural adjustments and the performance tests caused by external crises, the EU has experienced several reforms in recent years, affecting the competence of the EU's most important administrative institution, the EU Commission. In the EU's development, the intertexture of supranationalism and intergovernmentalism is the driving force behind the construction of EU governance. This study observes the institutional reform of the EU Commission from the angles of supranationalism and intergovernmentalism, with a focus on the Commission's competence enlargement and the checks and balances it faces. This study takes the Commission's performance in external trade policy and crisis management in recent years as case studies to explore the challenges that the Commission faces in governing the EU.