The Yellow River Delta is the youngest and best-preserved coastal wetland ecosystem in the warm temperate zone of China. The ecological security of the Yellow River Delta is seriously threatened by sea level rise and increased land subsidence, in the context of global climate change and intensified human activities. This paper evaluated the spatial and temporal characteristics of land use/cover and carbon stocks in the Yellow River Delta over the past 30 years, using the InVEST model based on eight periods of land use/cover data from 1991 to 2020. In addition, the seawater inundation model and PLUS model were used to predict the land use/cover and carbon stock patterns in the Yellow River Delta in 2035 and 2050, under the Ecological-Protection scenario, Natural-Development scenario and Economic-Growth scenario. The results showed that over the past 30 years, carbon stocks decreased by a total of 1079400 tonnes, representing a decrease of 8.12%. Natural wetlands and non-wetlands carbon stocks decreased by 3866600 tonnes and 185600 tonnes, respectively, and artificial wetlands carbon stocks increased by 2972700 tonnes. About 4.47%-11.58% and 6.20%-17.42% of the land in the Yellow River Delta will be inundated by seawater in 2035 and 2050, respectively, resulting in a reduction of carbon stocks in the Yellow River Delta in the future simulations of the three scenarios. The carbon stocks under the Ecological-Protection scenario, Natural-Development scenario and Economic-Growth scenario will decrease by 423800 tonnes, 766800 tonnes, and 1195000 tonnes, respectively by 2035, while by 593000 tonnes, 1190200 tonnes, and 1870100 tonnes, respectively, by 2050 for the three scenarios. The Ecological-Protection scenario has the lowest rate of carbon stocks reduction in the same period. The Yellow River Delta should prioritize green and sustainable development. On one hand, it is imperative to bolster the ecological protection of land use/cover types with high carbon storage and carbon fixation. On the other hand, effective measures such as controlling oil and underground brine mining, as well as backfilling mining areas, are essential for reducing land subsidence rates. Additionally, the construction of coastal dams in at-risk areas can mitigate the potential for seawater flooding, ultimately minimizing the loss of carbon reserves in the Yellow River Delta. The study points out that seawater inundation leads to huge loss of carbon stocks, which can provide data support and theoretical basis for improving the role of carbon sequestration and carbon sinks in the Yellow River Delta in the future.