Hydrological service is a hot issue in the current researches of ecosystem service, particularly in the upper reaches of mountain rivers in dry land areas, where the Qilian Mountain is a representative one. The Qilian Mountain, where forest, shrubland and grassland consist of its main ecosystems, can provide fresh water and many other ecosystem services, through a series of eco-hydrological process such as precipitation interception, soil water storage, and fresh water provision. Thus, monitoring water regulation and assessing the hydrological service of the Qilian Mountain are meaningful and helpful for the healthy development of the lower reaches of arid and semi-arid areas. In recent 10 years, hydrological services have been widely researched in terms of scale and landscape pattern, including water conservation, hydrological responses to afforestation and their ecological effects. This study, after analyzing lots of current models and applications of geographical information system (GIS) in hydrological services, gave a scientific and reasonable evaluation of mountain ecosystem in eco-hydrological services, by employing the combination of international forefronts and contentious issues into the Qilian Mountain. Assessments of hydrological services at regional or larger scales are limited compared with studies within watershed scale in the Qilian Mountain. In our evaluation results of forest ecosystems, it is concluded that long-term observation and dynamic monitoring of different types of ecosystem are indispensable, and the hydrological services and the potential variation in water supplement on regional and large scales should be central issues in the future research.