The internal organizational structure of the audit institution is the basis of the efficiency and effect of the audit work, and also determines the degree of realization of the audit objectives. Taking the provincial audit institutions as the research object, this paper analyzes the basic characteristics of their internal organizational structure and the theoretical logic of their changes. Based on the core knowledge requirements, the audit business department is set up according to the audit object, and the functions of the whole audit process should be performed by the audit business department, but based on the purpose of audit risk prevention and audit efficiency improvement, some audit functions are horizontally divided, and the performance of these audit functions is separated from the audit business department, and a special audit function is established, and the rest of the audit functions are performed by the audit business department.