An aquatic ecoregion-based assessment for water ecological security can offer a premise for the integrated management guidance of watershed ecological with the rule of “by type, by region”. Based on the natural features and social attributes of the spatial differentiation of ecological security pattern in basins on small and medium scales, the typical two tributaries in the northern Liaoning were selected as the study areas, i.e. the Qinghe river and the Fanhe river. On the basis of the third grade aquatic ecoregion, 6 elements including socio-economic pressure, environmental pressure, urban development indicators, development of resources and environment indicators, investment indicators, governance indicators were anlayzed and 13 indexes were selected according to the pressure-state-response model (PSR). The ecological security is divided into five degrees according to ecological security index by using the comprehensive ecological security index method, and they were specially insecurity, insecurity, basically security, security, special security.At the Qingheriver basin, ecoregion with codes of Ⅳ-5-9,Ⅳ-5-10,Ⅳ-5-11,Ⅳ-5-12,Ⅳ-5-14 are basically security and those with codes of Ⅳ-5-8 and Ⅳ-5-13 belong to insecurity. The ecoregions with codes of Ⅳ-5-1,Ⅳ-5-2,Ⅳ-5-3 of Fanhe river basin belong to basically security, and that with code of Ⅳ-5-4 is security. The results of aquatic ecoregion-based ecological security and grade division offer scientific references for water ecological protection and overall ecological management of Liaohe river basin.