This study addressed the challenges in managing higher education institutions (HEIs) in Vietnam amidst increasing autonomy. HEIs currently face limitations in financial dependence, ineffective human resource management, and slow curriculum reform, hindering sustainable development. This paper has shown that HEIs have significantly improved governance and adaptability to autonomy demands. However, challenges such as financial constraints, inefficiencies in human resource management, and outdated curricula remain significant barriers. From there, the paper proposed practical solutions to overcome these shortcomings. At the same time, the research results in the article not only strengthen the theoretical foundation of university autonomy but also provide practical arguments for improving management efficiency and promoting the sustainable development of the higher education system in Vietnam.