On August 16, 1999, HKUST, Peking University (PKU), and the Shenzhen Municipal Government jointly founded the PKU-HKUST Shenzhen Institution in the Shenzhen Hi-Tech Zone. The Institution was a breakthrough in collaborative ties between Hong Kong, Shenzhen, and a top university in Mainland China.

The Institution continues to play an essential role in research and development as well as education of rising talents.

Almost 20 years later, HKUST and PKU led multiple Hong Kong and Beijing universities to jointly establish the Beijing-Hong Kong Universities Alliance. The Alliance, founded in 2018, extends the strong ties among universities in the two cities.