Estuarine ecosystem is the ecotone between the river and ocean, which is under tremendous influences of concentrated human activities. Now, most estuarine ecological risk studies are based on the terrestrial ecosystem model, ignoring spatial heterogeneity distributing laws. This paper takes Daliao River as the study area and establishes a targeted estuary ecological risk evaluation model. Considering the scale request, the assessing technology mainly includes four steps: confirmation and analysis of study area, identification and analysis of risk sources, analysis of exposure and ecotoxic effects, and integrated estimation of ecological risks. Then the evaluation system is built up, which includes indices of biodiversity, afflux material, comprehensive pollution, and pressure index of socio-economic development. Combining the method of AHP, Principal Component Analysis and Polarized Standardization, the integrated index of ecological risk can afterwards be figured out. This model takes salinity and pollution sources as the major factors in the divisions of different sections and different water periods. And then this article effectively assesses the spatial distribution of ecological risk in Daliao River estuary, and explores the spatial and temporal distribution laws of estuarine ecological risk. The results show that, on the whole, the ecological risk of Daliao River estuary area is relatively high (the average risk value of three water periods is 0.56), which is over the middle level in 0 to 1 of the ecological risk index space; on time scale, the runoff is the main factor resulting in the ecological risk difference; on the spatial scale, the ecological risk index is affected by the pollutants carried by runoff of upstream, downstream pollution emissions and dilution water at the mouth the river together. In order to improve the environmental condition of the estuary area, more attention should be paid to the adverse effects of human activities on the estuarine ecosystem and improve the ecological conditions of the whole valley, thus the environmental problems of estuarine ecosystem can be solved fundamentally.