Spartina alterniflora has caused serious ecological problems in the coastal zone of mainland China. We used Landsat and HJ-1 satellite remote sensing images covering the Yellow River delta from 1989 to 2018 to quantitatively evaluate and understand the ecological effects of S. alterniflora invasion in the estuary delta. The remote sensing spectral indices normalized difference vegetation index (NDVI), fractional vegetation coverage (FVC) and modified normalized difference water index (MNDWI); the digital shoreline analysis system (DSAS) model; and the effective intertidal zone sedimentation width (EISW) analysis model were applied to these images. The effects on coastal protection, the impact on local vegetation ecosystems and the contribution to the greenhouse effect of S. alterniflora were studied. The main results showed that: (1) S. alterniflora invasion slows coastal erosion but, to achieve coastal stabilization, its distribution width needs to be greater than 700 m; (2) S. alterniflora invasion has caused serious degradation of local ecosystems. Among these, the area of Phragmites communis and Suaeda salsa decreased by more than 50%, and the seagrass bed ecosystem was seriously degraded; and (3) S. alterniflora invasion weakens the carbon storage capacity of coastal wetlands in the Yellow River delta, and intensifies the release of methane, reducing the ability of coastal vegetation wetlands to resist global warming.