In the context of global climate change，understanding the water budget and water conservation functions of typical ecosystems in the Qilian Mountains is of great significance for ecological protection and ecological security barrier construction in the west of China. Based on a long-term eddy covariance and hydrologic meteorological observation dataset in Heihe River Basin and Qinghai Lake Basin，we analyzed water budget changes and their characteristics in typical ecosystems（alpine meadow，alpine swamp meadow，Kobresia myosuroides meadow，Potentilla fruticosa shrubland，Stipa purpurea grassland，Achnatherum splendens grassland，desert，farmland，Tamarix chinensis shrubland，and Populus euphratica riparian forest）along an environmental gradient. The effects of biotic and abiotic factors on the water budget were analyzed and it showed that the budget varied significantly in different ecosystems in Qinghai Lake basin over a year. In all ecosystems，precipitation was greater than evapotranspiration during the growing season，while in the non-growing season it was the opposite. The average annual evaporation ratio（ET/P）of different ecosystems in Qinghai Lake basin in 2014～2015 was as follows：Kobresia myosuroides meadow（0.83）＜ Potentilla fruticosa shrubland（0.97）＜ Achnatherum splendens grassland（1.02），indicating that with increasing altitude，a declining trend was observed. The typical ecosystems of Heihe Basin had differences in water budgets，and different degrees of water deficit. In wet years，the upper alpine meadow water budget was basically balanced，while in dry years，the water deficit was about 134mm. The observed water deficit of the upper alpine meadow varied from 83 to 204mm over three years. The water deficit in the upper alpine meadow mainly comes from water supply outside the system（e.g.，glacier snow melt water，soil flow）. The farmland ecosystem water deficit is mainly charged by irrigation amount，which was 512 mm，554 mm and 560 mm，respectively，from 2014 to 2016. Groundwater and deep soil water are the replenishment sources of water deficit of desert，Populus euphratica forest and Tamarix chinensis shrubland. Drought index（DI=ET₀/P）and evaporation ratio（EI=ET/P）are both high for low altitude ecosystems. Evapotranspiration is mainly limited by water，and the proportion of precipitation runoff is very small. With increasing altitude，DI gradually decreases and EI rapidly decreases along the Budyko curve. Evapotranspiration gradually shifts from water limiting to energy limiting. The proportion of runoff to precipitation increases，and rapidly so with elevation，thus making the high-altitude area an important flow producing area of the basin. Recommendations are to：（1）improve water production capacity，and sustain the water conservation function of the basin，the alpine meadow ecosystems higher than 3600m should be vigorously protected，by reducing overgrazing and preventing damage of the mattic epipedon；（2）reduce soil erosion and improve water and soil conservation functions，the degraded Myricaria laxiflora valley wetlands should be restored through natural enclosure；and（3）optimize the spatial pattern and utilization of wetland in the life community of “mountain，forest，farmland，lake and grass system” using the concept of “mountain，water，forest，field，lake and grass” as the life community，combined with the construction of Qilian Mountain National Park.