The technology of freezing saline water irrigation (FSWI) with plastic mulching has been regarded as an effective way to reclaim the highly saline soil in coastal plains, which enabled the growth of crops in heavy saline soil that was not suitable for any crop growth before. However, after long-term treatment with FSWI, the microenvironment of the soil has been found to be affected by the growth of crops, which will directly influence the balance of soil carbon emissions. In this study, the characteristics of soil respiration in a typical saline field (planted with cotton) under four treatments (FSWI in Winter with plastic mulching, FSWI + Mulch; FSWI in Winter without plastic mulching, FSWI; plastic mulching in Spring without FSWI, mulch; no plastic mulching and no FSWI, CK) were investigated between June and November from 2015 to 2016. The results suggested that the soil surface temperature was an important factor that affected the soil respiration rate in each treatment during the growth period of cotton. FSWI + Mulch can reduce the soil surface salinity to 0.4% during the seedling stage, which increased the survival rate and the abundance of bacteria, fungi, and actinomycetes in the cotton field and subsequently increased soil respiration. By examining the effects of FWSI and mulching on soil respiration and its influencing factors, this study provides practical and theoretical insight into the sustainable development of agriculture in coastal saline plains.