Harmonious enterprise is the aim of the development. The construction of operation mechanism of harmonious enterprises is the important way of achieving harmonious enterprises, which is the explanation of the concept of scientific development and harmonious society. The paper analyzes the influential factors based on theory of coordinated original network. Then, the paper suggests building harmonious enterprise operating mechanism through the building of in-put and out-put sub mechanisms, harmonious enterprise operating sub mechanism and the coordinating and corresponding of the internal and external mechanism, which gives some insights into the research of principle parties to explore and the practice of harmonious enterprise operating mechanism.