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Adding gypsum and/or straw is a common practice for ameliorating saline-alkali soils. However, the effect of amendment on soil CO2 is poorly known. An incubation experiment was conducted for over two years in a saline-alkali soil of Yanqi Basin, which included four treatments: control, gypsum addition (Ca), wheat straw addition (S) and gypsum-wheat straw combination (Ca+S). We continuously monitored soil CO2 concentration, temperature and moisture at 15, 30, 45 and 60 cm. There was a clear seasonality in soil CO2 under all four treatments, which was generally similar to those in soil temperature and moisture. Straw addition led to a significant increase in soil CO2 over 0-60 cm in summer. While there was a significant increase of soil CO2 with gypsum addition only, soil CO2 significantly decreased with the addition of gypsum and straw (relative to straw addition only) during autumn and winter in 2014. Interestingly, integrated soil CO2 was lowest in soil profile under the Ca+S treatment during winter and spring. Our study implies that different amendments of organic matter and gypsum may result in various responses and interactions of biological, chemical and physical processes, with implications for the carbon cycle in saline-alkaline soils of arid region.