From the perspective of the roles and functions of Communist Party organization in state-owned enterprises, it is one of the most popular topics that Communist Party organization participates into the decisions on critical events in the enterprises. The exertion of decision-making mechanism called "Three Importance and One Great" gradually becomes the emphasized event, such as auditing of economic responsibility for the leaders in the enterprises, the essential contents of the assessment on responsibility system for Party conducts and incorrupt government, the inevitable reference on inspection, assessment and appraisal of appointment and remove. Communist Party organization is determined as the status of the political core in corporate government structure, which is the unique characteristic and fundamental requirement to the modern state-owned enterprises with Chinese features, as well as the component part of competitive power for the enterprises. In practice, the reform of state-owned enterprises has to face up to new difficulties. In this paper, authors make a survey by selecting many secondary corporations affiliated with state-owned enterprises for the analysis. At the aspects of corporate governance and practical construction in Communist Party, authors explore the structural relationships and operational mechanisms between corporate governance and Communist Party organization in state-owned enterprises through the application of embedding theory. Based on the scientific cooperation between the "central of operation" and "political core" in the state-owned enterprises, the concept of "co-governance from the internal and the external" is proposed to embed the supervision and punishment mechanisms into operational management system.