With the rapid development of the market economy, complex changes have occurred in the market environment, and the competition among enterprises has become extremely fierce. The transformation of the structure of the market economy has prompted enterprises to seek for new developments and innovations. Under the background of the new economy, enterprises must begin from the perspective of internal management and internal strategic development to ensure quality enterprise operation mechanism innovation. This would help direct enterprise operation and development as well as demonstrate the value of enterprise internal management. In this way, enterprises will be able to array their overall competitiveness. This paper comprises a detailed analysis of the connotation and innovation of enterprise operation mechanism under the economic transformation, with the purpose of investigating the innovation strategy of enterprise operation mechanism under the economic transformation.