The Yangtze River and Yellow River source regions are part of the highest and largest distribution area of wetlands in the world and play a key role in sustaining the ecosystem balance in this region. Current global changes, such as climate change and human activity, are significantly affecting the landscape pattern of these wetlands. These changes have had a major effect on the water cycle and ecosystem balance in this region and have attracted widespread attention. In order to clarify the characteristics of these changes, this research examines the temporal and spatial variation of the distributive patterns of the alpine wetlands in the Yangtze River and Yellow River source regions. The analysis was conducted by using aerial photographs taken in 1969 and Thematic Mapper remote sensing data obtained in 1986, 2000, 2007, and 2013. Additionally, a principal component analysis model and the gray correlation method were carried out using meteorological and human activity data to quantitatively analyze the contribution rates of climate and human factors to alpine wetland degradation. The relationship between alpine wetland degradation and environmental factors was determined. The results show that areas of alpine wetlands in the Yangtze River and Yellow River source regions have decreased by 19.16% from 1969 to 2013. However, the degradation rate of alpine wetlands has gradually decreased since 2000 in this region. Even the total lake area has rebounded from a previous decline and has been increasing since 2007. The spatial separation patch between each kind of alpine wetland increased. There were obvious differences in how the landscapes have changed in each source zone. In the Yangtze River's source region, the landscape change was mainly due to the disappearance of a small patch of wetlands from 1969 to 2007 and fragmentation of the large patch of wetlands since 2007. In the Yellow River's source region, however, the landscape change was mainly due to fragmentation throughout the entire study period. The degradation of alpine wetlands has mainly occurred in the northeastern Yangtze River source region and the northern Yellow River source region, which is consistent with permafrost degradation in this region. The climate in this region has been warming and drying with a significant increase in air temperature, decrease in the relative humidity, and slight increase in precipitation since 1969. There is obvious synchronization between alpine wetland degradation and climate change. Thus, the large increase in air temperature is considered the main contributor to alpine wetland degradation, while the rainfall and relative humidity changes have affected the wetland variation, particularly in the cases of rivers and lakes. The increase in livestock is the most important human factor in alpine wetland degradation. There are still some deficiencies in our research. First, the limited remote sensing data might not capture the inter-annual variability of the rivers, leading to large errors in estimation of river area variation. Secondly, the research reveals only the correlation between the change of wetlands and the various environmental factors by statistical methods, rather than clarifying the driving mechanisms behind them. Thus, future research should attempt to reduce the amount of error by accumulating more remote sensing data and focus on the driving mechanisms of various environmental factors on alpine wetland changes by using a community land model.