Cross-border water resources management which involves in regional and global economic and social development as well as world security has been an importance challenge in theory and practice at home and abroad. Academic discourses on cross-border water resources management are some of theoretical and practical significance, but there are problems as defined the core of management and so on. Based on the implementation of cross-border water resources management empirical analysis ,discussing the current issues of cross-border water resources management in the definition of the core problem and issues related to institutional arrangements ,the paper proposes that cross-border water resources management should establish systems and principles focusing on protection and preservation of “water quality“ and assessment and equitable distribution of “water quantity” as well as “ecological conservation” of drainage basin.