Innovative technology and deep uncertainty during the design and construction process of complex projects introduce great challenges to their organization and management. The traditional methods, represented in the project management body of knowledge (PMBOK) guide, can solve systematic problems; however, they cannot solve complex problems. Based on the management practice implemented in the deck pavement project of the Hong Kong-Zhuhai-Macao Bridge (HZMB), in this work, we propose a meta-synthesis management framework for a complex project from the perspective of the science of complexity. The method deems that the complexity of the project has the characteristic of being multi-scale both in the design phase and the construction phase. These problems can be classified into different categories, each of which requires a different strategy. As a result, it is first necessary to adopt the “exploration” strategy to reduce project complexity and to transform the deep uncertainty problems into systematic problems. Then, the “exploitation” strategy should be used to apply the PMBOK and other traditional methods to achieve the design and construction goals of the project and to improve its efficiency. More specifically, in the design phase of a complex project, the “innovative integration” process is used for the exploration of the new engineering technology and knowledge; then, the “functional integration” process is employed to define the system architecture, the interface relationship, the technical index, and other functions. In the construction phase, the “adaptive integration” process is used for the construction of the engineering organization system; next, the “efficient integration” process is employed to improve the actual construction performance. The meta-synthesis management framework proposed in this work reveals the multi-scale principle of solving complex problems in the management practice of a complex project, and develops the methodology of meta-synthesis.