Ecosystem management based on our best understanding of the ecosystem composition, the structure and function, and in definite spatiot emporal scales, it integrates human values and socialeconomic principles into managing ecosystems to restore and/or sustain ecosystem integrity and sustainabi lity. Under the direction of sustainable theory, it is the tendency to adopt the method of ecosystem management to develop and manage the international river ba sin comprehensively. Therefore, the concept and system of the international rive r basin management should be changed towards the systematic protection of the ri ver basin ecosystem. On the basis of analyzing the disadvantage of legal regime of comprehensive river basin management in the international water law, and also the weakness of regulations of protecting international water course ecosystem, which restricts the sustainable development of international river basin, the a uthor suggests that the comprehensive management of international river basin ma y satisfy the basic demand of human beings and also regard protecting ecosystem as its core duty, not separating the environmental resources in the river basin. The author also suggests that the international river basin management may pay attention to the protection of basin ecosystem systematically, especially the i nfluences of exterior factors, and the relevant economic and social issues may b e taken into account in the basin management. The author considers that the basi cprinciple of the international river basin ecosystembased management should m ainly include: principle of equitable utilization and no injuring foreign envir onment; principle of sustainable development; holistic principle; preventive pri nciple; principle of sharing basin information; principle of identifying or stip ulating thresholds; and principle of combining regional cooperation management together with the national management. The author also suggests simultaneously that some legal systems may be established as follows: comprehensive decisionm aking administration systems; estimating environmental influences systems; prote cting and distributing water resources in basin systems; ecoindustry and circu latory economic industry in basin systems; compensation to environment systems; recovering and rebuilding basin environment systems.