The index of biotic integrity (IBI) is sensitive to disturbance and can quantitatively describe the relationship between biological characteristics and the effects of human activities. It is one of the most widely used ecological indicators for evaluating aquatic ecosystem health. Originally, IBI was a type of water pollution assessment index that was established based on fish species composition, but it has now developed into a relatively complete evaluation system that has been used for the assessment of ecosystem health in bays, lakes, wetlands, forests, estuaries, and river systems. The comprehensive IBI index system based on fish has certain advantages over other evaluation indices because it includes information relating to fish population and individual status, as well as some aspects of community structure. Moreover, the IBI index system can be modified according to the objective and study area. In order to evaluate the biological integrity of the fish assemblage and the ecosystem health of the Yellow River estuary, bottom trawl survey data of fish species during 2013-2014 and historical data from the 1980s and 1990s were collected in the Yellow River estuary and its adjacent waters. A fish-based biotic integrity (F-IBI) index system for assessing habitat quality, which was originally developed by Karr, was proposed. The index system consists of 12 indicators that measure fish composition and richness, reproductive guild, and tolerance and trophic guild, taking into consideration the regional feature of fish species in Yellow River estuary. The evaluation criteria for F-IBI were also determined. Fish-based biotic integrity and habitat quality for the Yellow River estuary were evaluated. The results showed that the levels of fish biotic integrity in the Yellow River estuary during the 1980s, 1990s, and in 2013 were "excellent", "poor", and "very poor", respectively. Since the 1980s, the fish biotic integrity and environmental conditions have been declining in the Yellow River estuary. Anthropogenic activities such as overfishing have adversely affected the Yellow River estuary ecosystem and have led to the decrease or disappearance of fish species and decline of the ecosystem health of the Yellow River estuary.