Land is the most basic natural resources that mankind depend on for existence and development. Land cover change is the most obvious expression of the dynamic impact of human activities on land surface system, which will have an important impact on regional ecological environment and will influence the global environment cumulatively. Source regions of the Yangtze River (SRYA)and the Yellow River (SRYE) are important ecological protective screen in China,located in the Three-River Headwaters Region, which is known as the "Chinese water tower". In recent years, the land cover situation changed a lot due to climate change/human activities and some other factors. Based on the land cover datasets of middle and late 1970s, early 1990s, 2004 and 2012, this article analyzed the change characteristics of land cover and ecological situation and their differences in the SRYA and SRYE over the past 30 years, using the methods of transfer matrix, land cover situation index and land cover change index, and discussed the driving forces. The results showed that grassland were the main land cover types in both regions in 2012, but percentage of grassland in the SRYE was 17% more than that in the SRYA. In addition, there were glacier and desert in the SRYA, which was none in the SRYE. In the past 30 years, the land cover situation of the SRYE was better than that of the SRYA all the time. In terms of land cover change, the land cover and ecological situation of the SRYA became better, and had overall experienced a process of degeneration, slight melioration, and continuous melioration; while that of the SRYE became worse, and had overall experienced a process of degeneration, obvious degeneration and slight melioration, and the overall change in magnitude in the SRYE was more dramatic than that in the SRYA. Since there were huge glacier and permafrost in the SRYA, the warmer temperature since early 1990s made glaciers and permafrost melt, which made the water body and marsh expand and the land cover situation become better. The fact that land cover situation of the SRYE became worse in the period of 1970s and 2004 mainly because of overgrazing, warm and dry climate, while since 2004, the regional climate became warm and wet and that was helpful for natural ecosystem recovery. Meanwhile, reduction of livestock and the implementation of ecological project since 2004 also had certain positive effects on vegetation restoration in both source regions. Analysis on the different characteristics of land cover changes in the SRYA and SRYE will enhance our understanding of ecological environmental issues and changes in the SRYA and SRYE, and provide reference for the rehabilitation and reconstruction of integrated ecosystem functions in different areas.