Analyzing quantitatively the effect of vegetation canopy on rainfall partitioning is an important part for better understanding the hydrological cycle in terrestrial ecosystems, which is particularly useful for hydrologic budget estimation, hydrological models' establishment and afforestation projects' implement in drylands. However, it is difficult to measure and calculate its rainfall partitioning process of the natural vegetation in the drylands due to its sparse distribution and special morphological structure, and very few field measurements have conducted specially for the natural desert dwarf shrub species, which distributed widely in the oasis-desert ectone of northwestern China. Here we present results of the partitioning of rainfall into throughfall (TF), stemflow (SF) and interception loss (IL) by a shrub species Nitraria sphaerocarpa, a naturally dominant species of Linze oasis-desert ecotone in the middle part of the Hexi Corridor, based on the observation data during the growing season for 3 years. Consequently, the effective rainfall that actually enters the soil and its spatial distribution characteristics beneath the N. sphaerocarpa canopy are quantified. We also analyze the influencing factors for rainfall partitioning by N. sphaerocarpa canopy. The results show that: (1) on average, the measured throughfall, stemflow and derived interception loss by N. sphaerocarpa during growing season account for 87.89%, 1.61% and 10.50% of gross rainfall amount, respectively. The average funneling ratio for N. sphaerocarpa is (129.66 ±93.01) and its canopy storage capacity is 0.42 mm. N. sphaerocarpa's throughfall is produced from rainfall events with total amount more than 0.2 mm, while its stemflow does not occur following rainfall events less than 1.5 mm. (2) Rainfall amount is the key meteorological factor affecting the rainfall partitioning characteristics. There are significant correlations between rainfall amount and throughfall, stemflow and interception loss (P < 0.001). Other meteorological variables like canopy surface temperature, atmospheric temperature, atmospheric humidity and vapor pressure can also affect rainfall redistribution process. (3) Compared with other sparse vegetation in drylands, the N. sphaerocarpa has higher throughfall percentage and funneling ratio, but lower interception loss percentage. Special canopy morphology of N. sphaerocarpa may play an important role in its pattern of rainfall partitioning. Pearson correlation analysis shows that throughfall has significantly negative correlation with plant area index (PAI) and shrub height (P < 0.001), and stemflow has positive correlation with stem orientation (P < 0.01). Other canopy morphology like bark roughness, leaf shape and canopy form, which lack of quantitative description, are also vital for rainfall partitioning patterns. The results might improve better understanding of shrubs' role on the local hydrological processes in oasis-desert ecotone, and provide a reasonable method for estimating interception loss by sparse vegetation in drylands.