A new trend of government reforms of developed countries at the beginning of the 21st century is to promote institutionalized and effective cross-cutting cooperation, interagency coordination have consequently become the frontier areas in government reforms and international administrative studies. With the case of SHFTZ, we establish an analytical framework of “participant subject-administrative object-mechanisms” in terms of structural mechanism and procedural mechanism, so as to provide a new theoretical perspective for the innovation of FTZs’ government mode. It concludes that compared with procedural interagency mechanism, structural interagency coordination mechanism plays a key role in the administration of SHFTZ. Moreover, the construction of procedural interagency mechanism will improve and promote the effectiveness of structural interagency mechanism.