The nutrient-limiting conditions in saline–alkali soil as well as the salinity and alkalinity stress are successfully alleviated by water management measures and the addition of organic matter. However, the impacts of these two strategies on the microbe-driven CO2 emissions in saline–alkaline soils are not yet clear. Therefore, a 150-day incubation experiment was conducted in this study to evaluate the short-term effects of water regulation and the addition of organic matter with different characteristics on CO2 emissions and microbial community characteristics in saline–alkali soils under non-flooding conditions. This study was conducted at two water saturations, i.e., 50% WFPS and 80% WFPS. In addition, five organic matter treatments were conducted: CK: control; N: urea; SN: Straw + urea; SNH: Straw + urea + microbial agent; and SNB: Straw + urea + biochar. The results demonstrated that compared with 50% WFPS, 80% WFPS significantly increased cumulative CO2 emission by 27.66%, but significantly decreased salt content and the fungal Chao1 and Shannon indices. The application of the biochar and microbial agent decreased the cumulative CO2 emissions of the SN treatment by 27.39% and 14.92%, respectively. When sufficient carbon supply is available, the decrease in fungal diversity may reduce CO2 emission. The findings demonstrated that SNH and SNB at 80% WFPS might decrease CO2 emissions under straw carbon intake as well as the loss of labile organic carbon (LOC). Additionally, these treatments can alleviate microbial stress caused by salinity, which has a favorable impact on enhancing carbon storage in salinity-affected dryland soils.