Due to the impact of climate change and human activities, both the type and quality of ecosystems are changing in complex ways. As a result, ecosystem services and human well-being are profoundly affected. Nevertheless, how the ecosystem quality change affects ecosystem services is often neglected in previous studies. Compared with the dominant and obvious change in ecosystem types (or land cover types), the change of ecosystem quality is more subtle and continuous. However, the ecosystem quality change usually involves a much wider range, and may cause greater influence to the ecosystem resilience, function and services. Since Qinghai-Tibet Plateau is of great ecological importance and one of the most sensitive areas to climate change, it is desired to study the ongoing changes of the ecosystem and its services. Located at the south-east part of the Tibetan Plateau, Lhasa River Basin is the center of Tibet Autonomous Region in terms of economy, agriculture and demography. To reveal the recent ecosystem changes and the consequent service changes of Lhasa River Basin, especially the change in the ecosystem quality and its effects, we selected the growing season (from June to October) NDVI as the indicating factor of ecosystem quality to adjust the parameters of the InVEST model, and then assessed three ecosystem services (soil retention, seasonal water yield and carbon storage) from 1990 to 2015. The effects of the ecosystem type change and ecosystem quality change on ecosystem services, as well as their relative contributions, were then analyzed. The main conclusions are as follows:(1) from 1990 to 2015, the overall ecosystem type change was insignificant, and the change mainly occurred during the last 5 years. However, the area of artificial surfaces and wetland increased sharply by 82.65% and 32.40%, respectively. (2) The growing season NDVI of all vegetation types increased significantly between 1990 and 2000, and then slightly decreased afterwards. The growing season NDVI of meadow and grassland decreased by 7.48% and 5.44% respectively from 2000 to 2015, indicating an obvious degradation trend. (3) Overall, from 1990 to 2015, the ecosystem service changes caused by ecosystem type change were relatively small, while the ecosystem quality change had rather remarkable effects on the ecosystem services. From 1990 to 2000, the soil retention and carbon storage increased by 4.63% and 12.05% respectively, and the baseflow decreased by 22.14%; the contributions of ecosystem quality to these changes were 100.22%, 99.99% and -99.78% respectively. From 2000 to 2015, the soil retention, baseflow and carbon storage decreased by 0.62%, 1.17% and 2.62%, respectively; the contributions of ecosystem quality to these changes were -89.28%, 40.21% and -126.12% respectively; the contributions of land cover change were -10.94%、-140.26% and 27.44% respectively, indicating that the land cover change began to have greater effect on the ecosystem services after 2000.