In many arid ecosystems, vegetation frequently occurs in high-cover patches interspersed in a matrix of low plant cover. However, theoretical explanations for shrub patch pattern dynamics along climate gradients remain unclear on a large scale. This context aimed to assess the variance of the Reaumuria soongorica patch structure along the precipitation gradient and the factors that affect patch structure formation in the middle and lower Heihe River Basin (HRB). Field investigations on vegetation patterns and heterogeneity in soil properties were conducted during 2014 and 2015. The results showed that patch height, size and plant-to-patch distance were smaller in high precipitation habitats than in low precipitation sites. Climate, soil and vegetation explained 82.5% of the variance in patch structure. Spatially, R. soongorica shifted from a clumped to a random pattern on the landscape towards the MAP gradient, and heterogeneity in the surface soil properties (the ratio of biological soil crust (BSC) to bare gravels (BG)) determined the R. soongorica population distribution pattern in the middle and lower HRB. A conceptual model, which integrated water availability and plant facilitation and competition effects, was revealed that R. soongorica changed from a flexible water use strategy in high precipitation regions to a consistent water use strategy in low precipitation areas. Our study provides a comprehensive quantification of the variance in shrub patch structure along a precipitation gradient and may improve our understanding of vegetation pattern dynamics in the Gobi Desert under future climate change.