With the establishment of four special autonomous regions and provinces across the country, it is necessary to establish a relationship between local governments and local educational administrations in special autonomous regions and provinces that guarantees a high degree of autonomy. This study aims to explore the direction of desirable educational autonomy by examining the relationship between local governments and local educational administrations, focusing on educational administrators and examining what issues are in the relevant laws and regulations as well as what challenges need to be resolved in order to operate educational administrators that can fully secure educational autonomy and professionalism in special autonomous regions and provinces. As a result of this study, it was found that both the current Act on the Establishment of Special Autonomous Regions and related ordinances have constraints on local education autonomy and educational administrative audit, which may not sufficiently guarantee the political neutrality of educational autonomy and educational administrative audit, and may lead to inefficiency of educational administrative audit. Based on this discussion, it is suggested that the relevant laws should be revised to enhance the political neutrality and professionalism of local educational autonomy and educational administrative audit.