Mega project belongs to complex systems category and its overly complex system structure results in more management difficult. In order to improve management efficiency and complete project target, it is proposed to use new concept to identify and streamline size, scope and elements of mega project system, which is called effective large-scale system. Firstly, the concept of large-scale system and its effectiveness sources are defined. And then, the elements’ contribution degree and correlation degree criteria are presented. The contribution and correlation degree are based on fuzzy relationship matrix. Finally, coordination problems between the elements are solved by domination cooperative game model.