The Helan Mountain Eastern Foothills in Ningxia, China, a prominent viticultural region, exhibits significant heterogeneity in soil physicochemical properties and microbial communities, which collectively shape grape yield and quality. This study investigated seven Cabernet Sauvignon vineyards to unravel the interplay between soil parameters and microbial diversity-and their cascading effects on viticultural outcomes. Results revealed that soil structural metrics, such as macroaggregates (>0.25 mm) and capillary porosity, correlated positively with yield, while microaggregates (<0.25 mm) and aeration porosity showed contrasting relationships (p < 0.05). Dominant bacterial phyla, Actinobacteriota and Proteobacteria, were tightly linked to nutrient cycling and soil fertility, with Actinobacteriota abundance driving phosphatase activity and AP availability. Fungal diversity, influenced by soil texture and salinity, exhibited texture-dependent structuring, where high clay content suppressed fungal richness but enhanced water retention. Structural equation modeling (SEM) underscored the synergistic pathways through which soil physicochemical properties regulate microbial functionality (The GFI values for all models exceeded 0.50). The physical structure and water retention capacity of soil play a decisive role in the microbial habitat environment, especially for large aggregates with good water stability (AS>0.25 mm), which not only improve soil aeration and water retention, but also affect nutrient cycling and related enzyme activities (such as urease and phosphatase) by regulating the abundance and activity of specific microorganisms (such as Gemmatimonadota and Ascomycota). These findings highlight the critical role of soil health management in optimizing terroir-driven wine quality and yield, emphasizing targeted interventions for nutrient retention, aggregate stability, and microbial community balance within the Gypsic Calcisols and Calcaric Cambisols of semi-arid vineyard ecosystems.