Qilian Mountain is water source areas of Heihe River, Shiyang River and Shule River. The Heihe River as the second longest inland river in China has been paid more attention due to its eco-environmental problems. These problems include the continuous decrease in the discharge water of the Heihe River, desertification, salinization, and the increase of sand storms. Therefore, a series of conservation programs have been conducted for ecological environmental restoration in Qilian Mountain, especially in the upper reaches of Heihe River. To protect ecological environment of the upper reaches the natural reserve of Qilian Mountain has been established in 1989, Which plays a significant duty on conservation of natural vegetation. The shrub plays an important role in conservation water. The characteristics of the community are less studied. We selected Tianlaochi catchment in the upper reaches of Heihe River as study area and took the four typical alpine shrubs (Dasiphora fruticosa, Caragana jubata, Salix atrata and Spiraea alpine) as the study objects. We estimated aboveground biomass by remote sensing data combining with measurements. First, investigation was carried out in August of 2011 and 2012. We measured the shrub coverage, the height and biomass in many sampling points. According to the observed data, the relationship between biomass and coverage and height was built. Second, we collected remote sensing, such as airborne LiDAR (Light Detection And Ranging) and high-resolution remote sensing image (Geoeye-1). The LiDAR data was used to obtain the spatial distribution of shrub height. Geoeye-1 data was used to retrieve the spatial distribution of shrub coverage. Third, we calculated the spatial distribution of shrub aboveground biomass by the relationship and the spatial distribution of shrub height and coverage in ArcInfo. The results show that the relationship between the aboveground biomass and shrub height and coverage is a power function. The spatial distribution of aboveground biomass has great differences. The total aboveground shrub biomass is 141 t in study area; the maximum aboveground biomass unit area is 691.8 g/m². The higher aboveground biomass appears the zone with elevation ranging from 3300 to 3400 meters, which is the optimal habitat for shrub growth, the total aboveground biomass is 40.4 t in the zone. The aboveground biomass of shrub increases with the increase of elevation from 2655 to 3300 meters, nevertheless, it decreases with an increase of elevation from 3400 to 3750 meters. The variation of the aboveground biomass with elevation results from the combination of precipitation and temperature. Precipitation increases with the increase of elevation. Instead, temperature decreases with the increase of elevation. Form the study, we can draw some conclusions that the method to estimate shrub aboveground biomass is good way, it is useful to obtain higher accuracy carbon storage of shrub. In addition, two structure characteristics of shrub (i.e., height and coverage) can be used as important input information for hydrological spatial simulation in the subsequent researches.