Protecting the integrity and authenticity of ecosystems is one of the primary objectives of national park establishment and management. By scientifically assessing the degree of ecosystem integrity and authenticity, it becomes possible to determine conservation priorities in a rational manner. Such assessments provide critical scientific foundations for the rational allocation of resources, the identification of priority conservation targets, the delimitation of boundaries, and the delineation of functional zones within national parks. This study focused on the Yellow River Estuary National Park, China's first integrated land-sea national park, as its research area. In response to the current insufficiency of assessment research on its estuarine wetland ecosystem, which is predominantly governed by interactions among terrestrial, marine, and fluvial processes, and in combination with practical management demands, an evaluation system for ecosystem authenticity and integrity was constructed by selecting eight indicators based on the ecosystem "structure-process-function" theoretical framework. Furthermore, by comprehensively integrating remote sensing imagery and field survey data, the study area was delineated into two hierarchical levels comprising a total of 17 spatial units that exhibit significant differences in ecological characteristics. On this basis, a systematic conservation priority assessment was conducted for the natural ecosystems in the coastal zone of the Yellow River Estuary. The results indicate that ecosystems with high conservation priority are primarily concentrated in the following types: estuarine ecosystems, intertidal zone ecosystems, shallow marine ecosystems, salt marsh ecosystems, tidal flat ecosystems, seagrass bed ecosystems, shrubland ecosystems, riparian zone ecosystems, tidal creek ecosystems, and forest ecosystems. These ecosystem types generally perform high ecological connectivity functions or are situated in ecological transition zones, which results in their prominent ranking in the conservation priority evaluation. In contrast, ecosystem types such as river beach ecosystems, shell ridge ecosystems, river channel ecosystems, oyster reef ecosystems, supratidal zone ecosystems, swamp ecosystems, and grassland ecosystems exhibit relatively lower conservation priorities. Through the assessment, it was identified that these ecosystems commonly share the following pressures: intense anthropogenic disturbance, pronounced landscape structural fragmentation, and ongoing biodiversity decline. Based on the results of the ecosystem conservation priority sequence assessed for the construction zone of the Yellow River Estuary National Park, this study proposes a graded and classified conservation and restoration strategy, as well as a spatial zoning scheme oriented toward conservation priorities. These are intended to provide a scientific basis for the integrated land-sea ecological protection practices and high-quality development of the Yellow River Estuary National Park.