The hacker also reprogrammed pages of Tsinghua University's in-house course portal to display Arabic verses from Islamic scripture accompanied by music, a student newspaper at the Beijing institution reported.
Instead of displaying links to class resources and departmental information, the site showed a photo of four hooded fighters on horseback riding beneath the flag of ISIS, according to screenshots.
The cyber-intruder identified himself as an "Islamic State Hacker".
"God is great, I am unafraid of death, dying a martyr's death is my ultimate goal," reports translated an Arabic message as reading.
The student newspaper report was widely reposted by state-run media, but the original has since been deleted.
Mainland China operates some of the tightest online controls in the world, with content deemed to be sensitive deleted and access to some Western websites blocked.
China's far western region of Xinjiang is home to the mostly Muslim Uighur minority and the scene of sporadic, bloody violence which the ruling Communist Party attributes to separatist religious extremists with overseas links.
Critics accuse Beijing of discriminating against Uighur culture and religion.
Chinese state-run media have accused Uighurs of trying to escape the country to join terrorist groups abroad.
The department responsible for maintenance of Tsinghua University's website declined to confirm the incident to AFP.
Tsinghua, in Beijing, quickly shut down the server after the breach on Sunday evening was discovered, the reports said.
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