Multilevel governance (MLG) has been extensively applied to elucidate the dispersion of decisionmaking across multiple levels of governments—supranational, national, and subnational in the European Union (EU) and its member states. In this paper I attempt to contribute to the literature through the case of Hong Kong (HK) and the Pearl River Delta (PRD) in China. I argue that a pattern of MLG has been emerging since the early 2000s in this subnational-level cross-boundary region, accompanied by the gradual institutionalization of economic integration between Hong Kong and the PRD. Decisionmaking competencies in the HK–PRD cross-boundary region have tended to disperse across multiple levels of governments ranging from the central, Guangdong Provincial, HK Special Administrative Region, to municipal, city, and county level of the PRD, as well as businesses and residents on both sides of the boundary. In response to the lack of an effective regional authority and the unique political framework of ‘one country, two systems’, central government has played a somewhat backstage coordinator role in the transition of the integration mechanism and cross-boundary governance. Previous explanations of the integration and governance of the HK–PRD cross-boundary region need to be reevaluated. A regional level authority, similar to the supranational institutions in the EU, is urgently required to foster and upgrade cross-boundary cooperation.