Combining documentary analysis with hierarchical cluster analysis (HCA), we conduct a comparative study of innovation policies in two municipalities included in the Greater Bay Area (GBA) initiative—the Chinese government’s plan to link eleven cities into an economic and business hub. After identifying innovation policies/agencies in Hong Kong and Shenzhen, we apply the HCA to compare similarities and differences between their innovation policies and assess how these policies align with the ‘cross-border regional innovation system’ (CBRIS) conceptual approach.