Managing higher education facility in the context of autonomy is one of the inevitable trends in education in the current period. This work has achieved encouraging results, creating a healthy competitive environment, demonstrating capacity and significant changes in management. However, the management of university education institutions also faces many difficulties and challenges because higher education autonomy is one of the new mechanisms, implemented by many stages, managing many activities and requiring standards. For that reason, understanding the content of university autonomy and the advantages, challenges will help educational facilities prepare thoughtfully, promptly, remove difficulties, obstacles thoroughly and effectively.