Saline-alkali land poses a major threat to agricultural production and environmental protection in arid and semiarid regions. Under the combined effects of various factors, desert and oasis ecosystems coexist in these regions. However, the differential driving mechanisms of saline-alkali land in these ecosystems remain poorly understood. Taking the Hexi Corridor as a case study, large-scale field sampling was conducted, and multi-source environmental factors were integrated. Linear regression, elastic net modeling, optimal parameters-based geographical detector, and partial least squares path modeling were applied to systematically reveal the differential driving mechanisms of saline-alkali land in desert and oasis ecosystems. The results showed that average soil electrical conductivity in the desert system (6.493 dS/m) was significantly higher than in the oasis system (2.315 dS/m). Most environmental factors exerted significant individual influence on saline-alkali land. Moreover, the individual influence of factors in the desert system was overall stronger than that in the oasis system. Comprehensive path analysis indicated that precipitation (-0.489), soil physicochemical properties (0.394), soil microbial diversity (-0.213), and groundwater-dependent ecosystem density (0.129) exerted significant direct effects on saline-alkali land in the desert system. However, in the oasis system, soil microbial diversity (-0.667) and soil physicochemical properties (0.290) exerted significant direct effects. The study provides a scientific basis for zoned management of saline-alkali land in arid and semi-arid regions, with important implications for sustaining agricultural development and ecological security.