The emergence of interregional governmental cooperative agreements in the context of cross-regional flow of social factors is an inevitable trend in the transition from traditional administration to service-oriented administration. However, the legal academia has not conducted sufficient research on the typology of intergovernmental cooperation agreements, failing to promptly and effectively address new issues arising in administrative practice. The gap between theory and practice necessitates effective legal frameworks to bridge it. Therefore, after clarifying the legal positioning of interregional cooperative agreements, this paper identifies the existing legal issues and, guided by the values of whole-process people's democracy and law-based government administration, provides innovative approaches to improve the legal systems concerning the legal basis, content, procedures, supervision, and guarantees of such agreements.