Hong Kong-based Sun Wah Hi-Tech Group has agreed to team up with the Chinese Academy of Sciences to help develop the university's Red Flag Linux programme.
Sun Wah chairman Jonathan Choi said the company was the sole non-mainland strategic partner in the project, which is expected to compete with Microsoft in the mainland.
Mr Choi said Sun Wah, which started developing its Linux operating system a year ago, would provide technology and research support rather than funding in the first stage.
The parties have signed an agreement and will announce the details next week.
The State Natural Sciences Research Institute's Red Flag Linux project has an ambitious goal - it hopes to develop a true Chinese operating system and to compete with Microsoft.
Mr Choi said the project was fully endorsed and supported by the government.