The new era prompts engineers to consider both the current plight and the future development trend in the engineering industry. Based on the practice in Island & Tunnel Project of Hong Kong–Zhuhai–Macao Bridge, this article raised a new theory of Intrinsical Management and defined it from the aspects of practice and etymology. Then it proposed three factors and four connotations of Intrinsical Management, established its logical model, and elaborated its process and methodology taking the Island & Tunnel Project of Hong Kong–Zhuhai–Macao Bridge as an example. Intrinsical Management is a product deriving from engineering management practices in China, and it integrates Chinese management philosophy with eastern and western advanced management ideas. Intrinsical Management regards human as the most important factor, emphasizes dialectical and positive views, and gives full play to the initiative of human. It is an innovative methodology for solving complicated engineering challenges, and is forward-looking and dynamically applicable to engineering practices. Intrinsical Management presents a simple philosophy of “orientation emerging while root standing”, and has a pervasive significance in large-scale project construction and engineering management in China.