Based on survey data from fishery resources and on the ecological environment in the Jiaozhou Bay during 2015-2016 and 1980-1982, we constructed ecosystem models of Jiaozhou Bay for these two periods using Ecopath with Ecosim 6.5 software. The models of the Jiaozhou Bay consisted of 21 functional groups. Based on the two models, we compared and analyzed the differences in ecosystem structure, function, and attributes. The trophic structure of the Jiaozhou Bay ecosystem in 2015-2016 had changed, with a decrease in the proportion of top predator biomass and an increase in the proportion of R. philippinarum, and the mean trophic level of fishery catch had reduced. The energy flow of the Jiaozhou Bay ecosystem was mainly dominated by a grazing food chain, and the system-energy-transfer efficiencies increased from 15.83% in 1980-1982 to 16.35% in 2015-2016. Analysis of the keystones species for Jiaozhou bay ecosystem indicated that is a keystones species in both the 1980-1982 and 2015-2016 periods. Compared with the 1980s ecosystem, the scale of the Jiaozhou Bay system had increased and the net system production increased by 5 times by 2015. The parameters of the ratio of total primary production to total respiration increased from 1.267 in 1980-1982 to 2.518 in 2015-2016. In addition, the connectance index, system omnivory index, and Finn's cycling index decreased from the 1980s to 2015-2016. In conclusion, the maturity and stability of the Jiaozhou Bay ecosystem has been reduced over the past 30 years, and the system has shown a trend moving from a mature stage to an immature stage. In short, the Jiaozhou Bay ecosystem is currently in an unstable, young stage.