Abstract: Water resources allocation is a key topics for water resources development and utilization. The concept of optimal allocation of water resources based on ecosystem was presented. The developments and research methods were analyzed in the research of this area. Some technological difficulties were analyzed, i.e., eco-hydrological process mechanism, experimental data accumulation for ecological water demand, value of the ecosystem services, and hydrological theoretic basis of water resources allocation. The key topics which should be studied in the future, were also presented, i.e., eco-hydrological process mechanism, theoretic basis of ecological water demand calculation on basin scale, ecological value evaluation of water resources, distribution model of basin hydrology, and water resources evolvement law under the influences of natural and human factors, reasonable water resources allocation mechanisms based on ecosystem, and multi-sectoral regulation principle for water resources on basin scale and its decision-making methods.