Over the past decades, the development of knowledge-based and innovation-led economy has gained the attention of higher education (HE) institutions. The Quadruple Helix Model of the relations amongst universities, industries, government and society provides a general framework for systematically investigating the dynamics of innovation amongst these agents. However, knowledge about their influence on cross-boundary cities is limited. The ways in which HE institutions bridge different innovation systems also remain unknown. This study thus examines the innovation systems of two neighbouring cities along the border, namely, Hong Kong and Shenzhen, and their multidirectional innovation cooperation. Research findings suggest that the two innovation systems differ in terms of the unequal role of the agents. The systems seem mutually complementary in terms of HE capacity and industrial composition, and cross-boundary cooperation in HE sectors currently occurs through various means. This study sheds light on the development of and cooperation between cross-border innovation systems.