Saline water irrigation is a potential strategy to address agricultural water scarcity, but its effects on soil respiration and carbon balance are not well understood. To clarify these effects and promote the safe utilization of saline water resources, this study investigated five irrigation water salinity levels EC_iw: 1.3, 3.4, 7.1, 10.6, and 14.1 dS·m⁻¹ (i.e., 1, 2, 4, 6, 8 PSU; 1000, 2000, 4000, 6000, 8000 mg·L⁻¹) in a winter wheat–summer maize rotation during 2024–2025. The results indicated that saline water irrigation caused salt accumulation during the wheat season, whereas salt leaching occurred during the maize season. When EC_iw ≤ 3.4 dS·m⁻¹, no notable decreases were observed in dry matter accumulation, water productivity, and carbon emission efficiency for both crops. In contrast, when EC_iw > 3.4 dS·m⁻¹, the crop yields and net carbon input of the crop rotation system were suppressed to a considerable extent. Furthermore, under saline water irrigation, the average soil respiration rate decreased by 4.1–25.2% during the wheat growing season, while that for maize decreased by 7.4–30.7%. Soil respiration in wheat was negatively correlated with soil salinity and pH, and positively correlated with soil moisture (p < 0.01). In maize, soil respiration was negatively correlated with salinity (p < 0.01), and positively correlated with soil moisture (p < 0.05) and temperature (p < 0.01). The entropy-weighted TOPSIS model identified 3.4 dS·m⁻¹ as the appropriate irrigation salinity threshold for maintaining yield and carbon sink function in this rotation system.