Based on the grid analysis of GIS, with the combination of habitat suitability assessment and human interference analysis, the ecological sensitivity evaluation model was established. Firstly, the endangered water-birds in Yellow River Delta NNR were prioritized as a database according to IUCN 2007 Red List, and the habitat preference was identified and evaluated through literatures review and field survey. By establishing GIS-based 200m×200m girding system, the existing habitat was evaluated on landscape-level, and a Comprehensive Habitat Suitability Index (CHSI) was developed and calculated by habitat suitability assessment model. Based on CHSI, the habitat suitability was evaluated and graded. Secondly, the typical species Cranes was selected from the established database as indicator species and the habitat loss rate of indicator species associated with anthropogenic interference (roads and oil wells) was also analyzed on 200m×200m grids by GIS. Finally, on the basis of results from habitat suitability evaluation and human interference analysis, ecological sensitivity analysis was conducted by Overlying Operation. The results showed that: the ecological sensitivity of study area was quite high on the whole; the overall distribution was high in the coastal region low in the inland region, ranking in five classes of extreme sensitivity, fair sensitivity, moderate sensitivity, sensitivity and no sensitivity. In the area, extreme sensitivity zone and fair sensitivity zone accounted for about 55.74% in all, moderate sensitivity zone was about 16.2%, sensitivity zone and no sensitivity zone accounted for 22.81% and 5.19%, respectively. In addition, compared with existing function zones of reserve and combined with the research results, related suggestions for adjusting function zones were proposed aiming at enhancing the conservation efficacy of critical habitats.