The fractional cover of native grass species (NGS) and noxious weeds (NW) provides a more comprehensive understanding of grassland health in the alpine grasslands. However, coverage extraction of NGS and NW from satellite hyperspectral imagery can be challenging due to the small spectral and spatial feature difference, insufficient training samples, and the lack of effective fractional cover extraction methods. In this research, firstly, a feature optimization method is proposed to optimize the difference feature between NGS and NW. Secondly, a spectral-spatial constrained re-clustering training sample extension method (SSCTSE) is proposed to increase the number of training samples. Thirdly, a composite three-kernel SVM method (CTK-SVM) is developed to produce fractional cover maps of NGS and NW. The experimental results show that (1) the feature optimization method is effective in preserving the spectral and spatial difference features while eliminating invalid features; (2) the SSCTSE algorithm is capable of significantly increasing the number of training samples; (3) the fractional cover maps of NGS and NW are produced with the CTK-SVM method with overall accuracies of approximately 65%, and the RMSEs of NGS and NW are approximately 16% and 11%, respectively. The results provide a foundation for the fractional cover extraction of different grass species in alpine grasslands based on satellite hyperspectral imagery.