Large-scale coastal reclamation has caused significant changes in Spartina alterniflora (S. alterniflora) distribution in coastal regions of China. However, few studies have focused on estimation of the wetland vegetation biomass, especially of S. alterniflora, in coastal regions using LiDAR and hyperspectral data. In this study, the applicability of LiDAR and hypersectral data for estimating S. alterniflora biomass and mapping its distribution in coastal regions of China was explored to attempt problems of wetland vegetation biomass estimation caused by different vegetation types and different canopy height. Results showed that the highest correlation coefficient with S. alterniflora biomass was vegetation canopy height (0.817), followed by Normalized Difference Vegetation Index (NDVI) (0.635), Atmospherically Resistant Vegetation Index (ARVI) (0.631), Visible Atmospherically Resistant Index (VARI) (0.599), and Ratio Vegetation Index (RVI) (0.520). A multivariate linear estimation model of S. alterniflora biomass using a variable backward elimination method was developed with R squared coefficient of 0.902 and the residual predictive deviation (RPD) of 2.62. The model accuracy of S. alterniflora biomass was higher than that of wetland vegetation for mixed vegetation types because it improved the estimation accuracy caused by differences in spectral features and canopy heights of different kinds of wetland vegetation. The result indicated that estimated S. alterniflora biomass was in agreement with the field survey result. Owing to its basis in the fusion of LiDAR data and hyperspectral data, the proposed method provides an advantage for S. alterniflora mapping. The integration of high spatial resolution hyperspectral imagery and LiDAR data derived canopy height had significantly improved the accuracy of mapping S. alterniflora biomass.