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Engineering construction involves many internal factors and external environmental factors, resulting in conflict or uncoordinated problems in engineering management. The harmonious management of engineering construction is the process of coordinating and solving the contradiction between construction elements and the problems between them and the external environment. The connotations of three subsystems of engineering harmony, namely, Ren harmony (RH), Wu harmony (WH), and Shi harmony (SH), are defined, and the system architecture of engineering harmony is constructed. Then, a hypothetical model is proposed to deeply explore the impacts of subsystems such as Ren harmony, Wu harmony, and Shi harmony on engineering harmony, as well as the moderating effects of the natural ecology, social humanities, and political economy on engineering harmony. The results show that (1) natural ecology has a significant promotion effect on RH, SH, and engineering harmony; (2) social humanities have a significant enhancement effect on SH and engineering harmony; and (3) political economy does not play a significant role in any process. “Engineering harmony” is used to measure the effectiveness of engineering management, and a scientific scale is used to reflect this index. It provides a new idea for theoretical exploration and practical guidance in engineering construction management.