Saline water irrigation has been widely used for crop production where agriculture is short of freshwater. However, information about the response of soil respiration to saline water irrigation is limited. To identify the effect of saline water irrigation on soil respiration, the experiment based on long-term saline water irrigation cotton fields (since 2006) was conducted in the Heilonggang area in 2021. Five salinity levels in irrigation water were tested (3.4 [S1], 7.1 [S2], 10.6 [S3], 14.1 [S4], and 17.7 dS m⁻¹ [S5]), and deep ground water (1.3 dS m⁻¹) was used as the control (CK). After 15 years of saline water irrigation, we monitored soil physicochemical properties and soil respiration. In addition, we developed a structural equation model of the relationship between them. The results demonstrated that saline water irrigation significantly reduced soil water-stable aggregate content and porosity by 4.42–45.33% and 6.52–14.10%, respectively, and attenuated soil cellulase, α-glucosidase, and alkaline phosphatase activity. Soil respiration under saline water irrigation was significantly reduced by 5.28–33.08%. Moreover, saline water irrigation with salinity below 10.6 dS m⁻¹ had no significant effect on cotton yield. Moreover, soil salinity (62%), water-stable aggregate content (46%), and soil porosity (25%) had significant effects on soil respiration, and soil porosity had a significant positive effect on soil alkaline phosphatase activity according to the structural equation model. Overall, saline irrigation with salinity below 10.6 dS m⁻¹ can alleviate water shortages and reduce soil carbon emissions without affecting cotton yield in the study area.