Abstract: With the continuous development of higher education enterprise in China, the scales of higher institutions are expanding, which has put forward higher requirements to the financial management of colleges and universities. These situations generate the appointed accountant system in order to complete the deepened reform of financial management system in higher institutions. The appointed accountant system has played very important role in strengthening financial supervision, plugging financial holes, defending financial risks and preventing the loss of state assets, but there are also problems in the practical applications. In this paper, the author analyzes the basis and significance of appointed accountant system in higher institutions, presents the problems in the practice, and finally offers suggestions for the related problems in the case study of higher institutions under the Ministry of Education of the People's Republic of China.