Arid and semi-arid regions account for approximately half of China""s total land area. However, under the background of climate change, our understanding of the impacts of drought stress on aquatic organisms remains poorly understood. To investigate the effects of drought-related hydrological factors (DHFs) on phytoplankton, this study selected the Ningxia section of the Yellow River Basin - a typical area of aquatic ecological evolution in the arid and semi-arid regions of northwest China - as the research object. A total of 66 sampling sites were established in the main stream, tributaries, and affiliated lakes and reservoirs of this region in autumn (October) 2023, and an aquatic ecological survey was conducted. Hierarchical cluster analysis, non-metric multidimensional scaling (NMDS), and analysis of similarity (ANOSIM) were used to investigate the spatial distribution pattern of phytoplankton communities and the differences among groups. Multiple statistical methods, including Mantel test, redundancy analysis (RDA), and variance partitioning, were employed to systematically decipher the response mechanisms of phytoplankton to DHFs. As a result, a total of 143 phytoplankton species (including varieties) belonging to 7 phyla and 81 genera were identified. The community structure exhibited typical diatom-chlorophyte characteristics, with diatoms accounting for 39% of total species and 47% of total biomass. Significant spatial heterogeneity of DHFs was observed in the study area, with coefficients of variation (CV) for turbidity, TN/TP mass ratio, and total dissolved solids (TDS) reaching as high as 2.04, 2.03, and 1.66, respectively. Correspondingly, the CVs of phytoplankton cell density and biomass were 1.84 and 1.42, respectively. The average TN/TP mass ratio in the study area was 91.15, indicating clear phosphorus limitation. Hierarchical cluster analysis based on Bray-Curtis distances divided the phytoplankton communities into four groups with highly significant spatial heterogeneity (ANOSIM: R=0.783, p=0.001), and all DHFs differed significantly among groups. Mantel test and RDA results indicated that pH, turbidity, chemical oxygen demand (COD), and total phosphorus (TP) were key drivers of changes in phytoplankton community structure. Variance partitioning showed that DHFs alone explained 12% of the community variation, which was six times the explanatory power of other factors (e.g., traditional nutrients, 2%). This study confirms the potential impact of drought on changes in phytoplankton community structure and provides a new perspective on the mechanisms underlying spatial pattern formation of phytoplankton communities in arid regions.