Based on the principles of protecting integrity and stability of ecosystem, and aimed at promoting maintenance of well-conditioned delta ecosystem, as well as improving the carrying capacity of the ecosystem and protecting biodiversity, this paper identified 23,600 hm2 of wetlands for restoration project which urgently needed to be supplied with freshwater in the Yellow River Delta (YRD). Whereas, this paper, adopting the principle and methodology of landscape ecology and supported by RS and GIS and wetlands plant physiology, ecology and hydrology, made a study on coupling mechanism between water and ecological process, and therefore, established the eco-hydrology based environmental flow calculation and evaluation model of the YRD. Furthermore, this study uses pre-scheme methodology and planning evaluation concept of landscape ecology decision & evaluation support system to forecast and evaluate ecological effects on the wetlands with different wetlands water discharge scenarios, which focused on the relationship study between suitable habitat conditions for indicator species such as red-crowned crane, Oriental stork, Sauder's gull and changing ecological pattern after water supplement. The evaluation results show that the wetlands of the YRD have the potential to be the habitat for rare birds such as red-crowned crane, Oriental stork, Sauder's gull, but the present habitat quality is not good. After discharging water to wetlands, the area of reed wetlands will reach 22,000 hm2 from 10,000 hm2 and seablite mudflats will reach 7000 hm2 from 4500 hm2, serving as wintering, inhabiting and breeding sites for many rare birds. The habitat quality and carrying capacity will increase notably. In general, after fully taking into account water resources, water allocation engineering measures and integrated requirement of wetlands ecosystem protection, this study proposed recommendation of supplying the wetlands of the YRD with 0.35 billion m3/a freshwater abstracted from the Yellow River to restore and protect the YRD wetlands ecosystem.