The tuition fee of the institute is RMB 56,000 a year and the accommodation fee (quadruple room) is RMB 1500 a year, which are all approved by the Ministry of Education of the People's Republic of China.

Nanjing Audit University has established national scholarship, auditor-general scholarship, principal’s scholarship, comprehensive scholarship, programme-studying award, new students scholarship, etc.  Students of the International Joint Audit Institute can declare all the scholarships above. In addition, the institute establishes its own individual scholarships. Students can contest both the scholarships offered by the university and the scholarships offered by the institute at the same time, with a winning percentage of up to 40%.