In the context of population growth and climate change, the scarcity of water resources has being more prominent,making development and utilization of transboundary river an internationally and regionally sensitive and intractable problem. The competition over transboundary river water resources is aPrisoner Dilemmasituation. This paper explored the way of applying reciprocity theory on untacking Prisoner Dilemma in transboundary river cooperation, and discussed its feasibility and prerequisites. The case of Nile River in Africa was studied to analyze the challenges in transboundary river cooperation, and then the way towards evolution of cooperation was proposed. The Columbia River in North America was taken to exemplify the way towards evolution of cooperation on transboundary river cooperation. The results show that reasonable exploitation of transboundary river could not only increase common benefit of upstream and downstream states, but also promote the evolution of international cooperation in political and economic areas. Successful practice of reciprocity theory provides reference for cooperation policy making in water resources area between China and neighboring countries.