With the regional population growth, socioeconomic development, more and more attention has been paid to issues on the shared water allocation and the transboundary eco-security conservation during the development of water resources in the international rivers. In this paper, the existing major problems on transboundary waters in different sub-regions of Asia, such as water shortage, transboundary waters pollution, fragile eco-environment are discussed. Then, the key scientific issues to be concerned in the next study progress on the basis of the analyses of the new research directions and focus fields are raised: (1) unpredicted changes of the hydrologic and water system, and their impacts on the allocation of the sharing waters by global changes; (2) models of the international cooperation on the international rivers on the studies of international and national water laws or regulations, policies, the relative experiences and the case studies; (3) quantificational assessment on environmental flow, available water, and the comprehensive functions and values of the international watercourse system; (4) studies on transboundary aquatic bio-diversity maintenance, transboundary pollution supervision and treatment under the rules and principles accepted by the riparian states; (5) issues on transboundary compensation at the rules of “payments for using”, “payments for harm” and “compensation for benefit”; (6) using advanced 3S techniques to promote the integrated watershed development and management; and so on.