The unique desertification under alpine climate and ecosystem on Tibetan Plateau could provide critical clues on the natural and anthropogenic impacts on desertification. This study used the Landsat data to investigate the distributions of desertification from 1990 to 2020 in two areas (Shannan and Mainling), within the Yarlung Zangbo River Basin. The results show not only different spatial distributions but also various temporal changes of desertification. In Shannan, aeolian sand is distributed in wide areas from valley floor to mountain slope, while in Mainling, it is distributed sporadically at the footslope. The aeolian sandy land expanded at first, followed by a long-term shrinkage in Shannan. While in Mainling, it steadily expanded and then followed by a fast decrease. These changes are attributed to climate change and anthropogenic factors. The increase in temperature causes desertification expansion in Shannan, while favorable climate along with decreasing human activity promotes desertification reversal. However, both the expansion and shrinkage of desertification are sensitive to human activity in Mainling. This show diverse responses of desertification to natural and anthropogenic impacts on different backgrounds of climatic and vegetation coverage. A threshold of climatic conditions could control the dominant factor in desertification from natural to anthropogenic elements.