Abstract: Yellow River Estuary and adjacent waters are famous shellfish production areas. Mactra veseriformis, Ruditapes philippinarum, and Meretix meretrix are important species for stocking enhancement. At present, the annual output of shellfish bottom sowing culture has reached 300 thousand tons, with an output value of 1.54 billion RMB. Over stocking of shellfish will cause environmental changes in marine, increase shellfish mortality and endanger ecosystem health. Accordingly, the assessment of the carrying capacity for shellfish based on ecosystem underpins responsible marine fisheries enhancement. In this study, an Ecopath mass-balance model of the Yellow River estuary and adjacent waters ecosystem constructed by Ecopath with Ecosim software was used to analyze the summary statistics parameters of the ecosystem, mixed trophic interactions, and to calculate the ecological carrying capacity of shellfish. The results showed that the ratio of total primary production/total respiration (TPP/TR) was 3.45, that of total primary production/total biomass (TPP/B) was 38.91, with the low Finn cycling index (0.028), high surplus production being 961.24 t·km^-2·a^-1 and low system connecting index (0.38), indicating that this ecosystem was at an unstable development stage. The increases of shellfish biomass would have positive impacts on Gobiidae, shrimps, crabs, and negative impacts on pelagic fishes, demersal fishes, edible jellyfish, zooplankton. Current biomass of shellfish was 5.5 t·km^-2, with the potential enhancement. Based on the Ecopath model, the primary assessment of carrying capacity of shellfish was 18.22 t·km^-2 in Yellow River estuary and its adjacent waters. This study provides scientific references for the sustainable development of fisheries resources in the Yellow River estuary.