Habitat quality is one of the significant ecosystem services, and studying the coupling relationship of habitat quality-pattern-process is of great significance to the maintenance and sustainable management of regionally ecological functions. In this paper, the core area of Yancheng National Nature Reserve in Jiangsu province being taken as the research object, we assessed the habitat quality by using InVEST model, discussed the relationship between habitat quality, landscape pattern and ecological process, and simulated the spatial-temporal change of habitat quality by using multiple regression model and landscape process model based on the remote-sensing images in 1992, 2000, 2011 and 2017 and the soil moisture/salinity in 2011. The results showed that: 1) from 1992 to 2017, the area percentage of Phragmites australis marsh increased from 0.13% to 36.95% and the area percentage of Spartina alterniflora marsh increased from 3.05% to 35.42%. The area percentage of Suaeda salsa marsh first increased and then decreased to 5.11%. 2) from 1992 to 2011, the habitat quality index decreased from 0.85 to 0.76, with a decrease of 10.52%. From 2011 to 2017, the change of habitat quality index was opposite to that from 1992 to 2011, and the habitat quality index increased to 0.78. 3) the results of multiple regression analysis showed that: the ecological process and landscape pattern were significantly correlated at the significance level 0.01, indicating that landscape pattern and ecological process were interactive. When the significance level was 0.10, the habitat quality was significantly correlated with the ecological process and landscape pattern, and the overall correlation coefficient was 0.69. 4) the results of landscape pattern and habitat quality simulation showed that the area percentage of Spartina alterniflora marsh would expand to 64.06%, and that of Suaeda salsa marsh area would decrease to 0.04% by 2030. Habitat quality index would decrease to 0.65. The expansion of Spartina alterniflora is the main reason for the decline of habitat quality. Constructing the coupling relationship of pattern-process-quality can control the expansion of Spartina alterniflora from the ecological process. It's necessary to change the regional landscape pattern and optimize the habitat quality, thus providing reference for the protection and construction of world natural heritage sites.