Engineering is an important and complex activity during the process of human survival and development, and to enhance its management effectiveness is the key to ensure social development. The current engineering activities appears a series of discord and lack of innovation, such as less integrated innovation, frequent accidents, and so on. The core of enhancing the effectiveness of engineering management is that the manager can achieve interactive development of harmony and innovation on the basis of perfecting engineering harmony and innovation. It defines engineering harmony and innovation, and then proposes that harmony is the new starting point and final goal of innovation; conversely, innovation is the motive power for the maintenance of harmony, and the drive for achievement of a higher level of harmony. Research on interaction between harmony and innovation is conducive to change our traditional view of engineering innovation, pursuit the harmony in inner organization and harmony of engineering and ecological environment and meet the needs of sustainable development.