Effect of sand-fixing shrubs on water redistribution is a key link in the water cycle in sandy areas. However, previous studies have not sufficiently focused on the coupling analysis of the aboveground morphology of these shrubs with throughfall (TF) and soil evaporation (SE), limiting the accurate assessment of their water-holding effect. This study focused on three sand-fixing shrubs, Salix psammophila, Artemisia ordosica, and Caragana korshinskii, along the eastern edge of the Hobq Desert, investigating TF and SE changes under varying rainfall conditions and across different spatial environments. The water-holding index (W) of these shrubs was analyzed in response to rainfall and its correlation with the aboveground morphological traits. Results indicate that under 5.8 mm rainfall conditions, the W values for S. psammophila and C. korshinskii ranged between –0.1 and 0.0 while those for A. ordosica ranged from 0.03 to 0.08. During heavy rainfall (> 10.7 mm), the W values for all shrubs increased to between 0.00 and 0.17, illustrating the enhanced water-holding effect of shrubs under such conditions. Shrub configuration factors, such as the ratio of the branch diameter (RBD), overall branching rate (OBR), and branch ground angle, were well-fitted to W. RBD and OBR were the main factors influencing the water-holding effect of sand-fixing shrubs, explaining 77.3% of the variation in W for sand-fixing shrubs. This study highlights the pivotal role of shrub morphology in regional water cycles, revealing that shrubs with a higher OBR and RBD and smaller branch-to-ground angle exhibit a superior water-holding effect.