Taking the typical alpine shrubs Potentilla fruticosa, Salix cupularis, Hippophae rhamnoides, and Caragana jubata in Qilian Mountain as test objects, a field investigation from June 1 to October 31, 2010 was conducted on the variation characteristics of the shrub stemflow, and analyzed the affecting effects of rainfall intensity and canopy structure morphology. The stemflow generated when the rainfall in early period was 2.1 mm, with an average of 3.4%, 3.2%, 8.0%, and 4.2% of the gross rainfall for P. fruticosa, S. cupularis, H. rhamnoides, and C. jubata, respectively. There was a significant positive linear correlation between the stemflow and rainfall intensity. With increasing rainfall, the stemflow percentage showed a trend of increase-decrease-increase. Stemflow played an important role in supplying water to the shrub rhizosphere, and the average funneling ratio was 59, 30, 110, and 49 for P. fruticosa, S. cupularis, H. rhamnoides, and C. jubata, respectively. The stemflow percentage had a significant exponential relationship with the maximum rain intensity in 10 minutes (I10). When the I10 was more than 6.0 mm x h(-1), the stemflow of H. rhamnoides and C. jubata showed a persistently increasing trend, while that of P. fruticosa and S. cupularis tended to be stable. Canopy structure morphology had complicated effects on the stemflow. In the same rainfall intensities, the height and crown projection area of the shrubs were the important factors affecting the generation of stemflow.