The Yancheng coastal wetland is an important part of migratory bird habitat along the coast of the Yellow Sea-Bohai Sea of China. Habitat quality is an important reflection of habitat function, while the expansion of Spartina alterniflora has seriously threatened the migratory bird habitat. Therefore, based on the remote sensing images of 10 time periods from 1983 to 2017 and employing image processing and GIS technologies, the relationship between the spatial-temporal variation of habitat quality and the expansion of Spartina alterniflora in the core area of the Yancheng National Nature Reserve was analyzed by using the InVEST model. The results are as follows: (1) From 1983 to 2017, there was a significant positive correlation between the expansion of Spartina alterniflora and time, and the percentage of the area of Spartina alterniflora marsh increased from 1.693% to 24.930%. It clearly went through several stages in time, and the expansion of Spartina alterniflora showed multi-directional and spatially variable characteristics. (2) Under the influence of human activities and the expansion of Spartina alterniflora, migatory bird habitat quality showed obvious fluctuations: From 1983 to 1988, habitat quality index value increased from 0.863 to 0.878, then decreased to 0.740 in 2014 and increased again to 0.775 in 2017. (3) There was a positive correlation between the areal change of Spartina alterniflora marsh and the change of the index of habitat degradation, and a negative correlation between the areal change of Spartina alterniflora marsh and the change of the index of habitat quality. The expansion of Spartina alterniflora led to the dramatic decrease in area of the Suaeda salsa marsh, which is a regionally suitability habitat, and this became an important factor in the degradation of regional habitat quality. Therefore, controlling the expansion of Spartina alterniflora is an important problem faced by the region. The results can provide reference for the improvement of habitat and sustainable management of coastal wetland from the perspective of the relationship between landscape pattern and habitat quality.