Wuyi University was granted the authority to confer master's degrees in 1998 and has the qualification to accept outstanding undergraduate graduates recommended for exemption from the graduate entrance examination. It currently offers 7 first-level disciplines for master's degree conferral and 7 categories for professional master's degree conferral, with master's degree conferral points covering all science and engineering disciplines of the university.

The university has a graduate faculty team with strong political qualities and academic strength. There are 26 high-level talents at the national and provincial levels, with 10 individuals selected for the list of the top 2% of the world's leading scientists; 48 doctoral supervisors and 505 master's supervisors; more than 100 corporate mentors with strong capabilities in solving complex engineering problems have been selected to participate in the guidance of professional master's students.

WYU collaborates with institutions such as Jinan University and the University of Macau to jointly cultivate doctoral students in disciplines such as biomedicine and materials science. Several outstanding graduate students are annually selected to study and engage in exchanges at renowned universities including the Hong Kong Polytechnic University. WYU promotes the integration of science and education, which has selected more than 90 graduate students for the joint cultivation with the Guangdong Provincial Academy of Sciences. Additionally, integration model of industry and education has been constructed by establishing the CIMC Modern Industry College with leading enterprises like CIMC and setting up more than 40 off-campus joint training bases for graduate students.

The quality of graduate education at the university continues to improve. In the random inspection of master's theses conducted by the Guangdong Provincial Department of Education, the annual inspection results have all passed with a 100% pass rate, and the rate of excellence is over 90%. In the past three years, students have published more than 410 high-level papers in the SCI Q2 and above categories. The number of students pursuing further studies has been steadily increasing, with the doctoral enrollment rate for the class of 2024 exceeding 10%.