Implementing Decree No. 43/2006/ND-CP dated 25/04/2006 by the goverment and guiding circular No.71 /2006/TT-BTC by the Ministry of Finance on 9/8/2006, it's regulatrd that public universities are autonomus, self responsible for tasks, organization, staffing, and finance. The result of financial autonomy policies have given advantage for higher education establishment in financial management in comparison with the previous mechanism. Beside the achieved results, implementing Decree No.43/2006/ND-CP of financial autonomy still exists some obstacles and difficulties for higher education establishment. In order to improve the financial autonomy the goverment shall issue additional policies to building tuition fee, increase revenues, revenues utilization, crucial investment procedure etc. to create a legal framework for institutions of higher education to implement. Besides financial autonomy, it must be attached with the regulation of inspection and supervision of the responsibilities of institutions of higher education. Thereby, institutions of higher education could ensure to provide good quality of higher education for students.