Saline water irrigation is an increasingly critical strategy for mitigating water scarcity in oasis agriculture. However, its impact on soil health at the aggregate scale, particularly concerning carbon sequestration and microbial communities, remains poorly understood. We conducted a four-year cotton field experiment irrigated with water at four salinity levels: CK (0.87 g·L⁻¹), T1 (3 g·L⁻¹), T2 (5 g·L⁻¹), and T3 (8 g·L⁻¹). Results indicated that increasing salinity elevated aggregate levels of salt cations (K⁺, Ca²⁺, Na⁺, Mg²⁺), total nitrogen, soil organic carbon (SOC), and labile organic carbon (LOC). In contrast, total carbon (TC), inorganic carbon (SIC), and microbial biomass carbon (MBC) decreased. While saline irrigation reduced soil fungal diversity, it did not significantly alter bacterial diversity. Microbial diversity was also strongly influenced by aggregate size, with the highest fungal richness and bacterial diversity found in the < 0.25 mm fraction. Network analysis revealed that increasing salinity simplified bacterial community interactions but increased the proportion of coexisting species; fungal community networks showed no significant trends. Redundancy analysis identified SOC, LOC, TC, and Na⁺ as the primary factors governing both bacterial and fungal communities, with base cations and carbon fractions exerting a stronger influence on fungi. Based on the effects of saline water irrigation on the stability of microbial diversity and composition, we recommend a salinity threshold of ≤ 3 g·L⁻¹ to maintain sustainable crop yield and soil structural stability in regional cotton fields. This study provides a critical scientific foundation for optimizing saline water irrigation management in oasis ecosystems.