Infrastructure mega-projects (IMP), which involve complex interactions and feedback, have more significant impact on economic, social, and other systems. This paper proposes a concept—the IMP complex ecosystem—to analyze IMP from a broad perspective of organic links across engineering, social, economic, and resource environments. Moreover, this paper proposes the theoretical concept, framework, and functions for the IMP complex ecosystem based on complex ecosystem theory. First, the coupling process between IMP complex ecosystem subsystems is analyzed through material flows, energy flows, information flows, and value streams. Second, a logistic model of the IMP complex ecosystem is proposed by analyzing the evolution conditions and motivations. Third, the evolution pattern of the IMP complex ecosystem is determined. Fourth, the positive evolution strategy of the IMP complex ecosystem based on dissipative structure theory and the influencing factors of the evolutionary process is introduced. Finally, the Hong Kong-Zhuhai-Macao Bridge and Sousa chinensis are used as the case study. This paper also analyzes the coupling structure on the complex ecosystem of the Hong Kong-Zhuhai-Macao Bridge and investigates the coupling and evolution mechanism application of the IMP complex ecosystem on Sousa chinensis protection for the Hong Kong-Zhuhai-Macao Bridge project.