Since the establishment of the Free Trade Zone（FTZ），there has been obvious development in cross-departmental cooperation，promoted by the law enforcement agencies of trade regulation，in which the Customs plays a major role. However，there are also some problems，including operational coordination，propelling initiative，coverage of business，standard uniformity，informatization，and foresight of system. These problems can boil down to lack of momentum and insufficient capacity. Therefore，it is highly recommended to perceive from organizational reform theory and mechanic analysis，and consider solutions from the power boost，resistance reduction and capacity improvement，so as to deepen cross-departmental cooperation in trade regulation in Shanghai Free Trade Zone.