The establishment of free trade zones marks a significant milestone for Taiwan in its efforts to advance global logistics operations, pursue trade liberalization and internationalization, enhance national competitiveness, and drive economic development. This study delves into the legal framework governing Taiwan's free trade zones and analyzes the challenges and issues encountered in their practical implementation. Since the enactment of the Free Trade Zone Act in 2003, Taiwan has established six maritime free trade zones aimed at promoting trade liberalization and internationalization to enhance the nation's economic competitiveness. However, research findings indicate that the operation of these free trade zones faces various legal and administrative challenges. Firstly, the procedures for goods clearance and entry/exit permits are cumbersome, involving multiple departmental reviews and complex documentation requirements. This results in high time costs, negatively impacting logistics efficiency and the attractiveness of the port zones. Secondly, the rigidity of the management system hinders its ability to adapt to the rapidly changing international trade environment, particularly in responding to unexpected business demands. Additionally, the inadequacies of the electronic system further reduce information processing efficiency, affecting overall management and coordination effectiveness. The study recommends accelerating the legislative reform process to improve management efficiency through measures such as streamlining procedural workflows, enhancing digitalization, and strengthening interdepartmental coordination. These improvements aim to boost the international competitiveness of free trade zones, positioning Taiwan as a key global trade hub and preventing the marginalization of its port economy. Such measures are essential to securing Taiwan's critical role in the global supply chain.