Saline–alkali soils in arid regions are increasingly recognized as critical yet underrepresented components of the global carbon cycle. However, their CO₂ flux dynamics under warming remain poorly understood. In this study, we conducted controlled growth-chamber experiments using typical saline–alkali soils from the Taklamakan Desert, where temperature, soil moisture, and atmospheric CO₂ concentrations were systematically manipulated. We quantified how warming reshaped moisture–temperature interactions regulating soil CO₂ fluxes. The results revealed a pronounced diurnal variation pattern, characterized by daytime CO₂ release and nighttime uptake. Temperature was identified as the dominant driver (R² > 0.93, p < 0.001), whereas soil moisture primarily modulated flux intensity; at 0.8 cm³ cm⁻³, fluxes declined by up to 61% compared with the baseline. Warming enhanced the temperature–moisture synergy (−43%, p < 0.01) and simultaneously reduced baseline fluxes (−56%, p < 0.01). These shifts fundamentally altered the regulation of CO₂ flux dynamics. Our findings highlight the necessity of integrating salt dynamics and carbonate equilibria into multiphase reactive transport models to improve regional carbon sink assessments. Ultimately, this study refines estimates of the contribution of saline–alkali soils to the global “missing carbon sink” (~1.7 Pg C a⁻¹) and emphasizes their overlooked role in the Earth’s carbon budget under a warming climate.