The greenhouse effect induced by elevated CO₂ can be alleviated by increasing capacity of carbon (C) sequestration in terrestrial ecosystems. Here, we carried out an indoor column simulation experiment with saline and sodic soils to assess the responses of ecosystem C stocks (including the C stock in soil and plant biomass) under the different amounts of flue gas desulfurization gypsum (FGDG) application (0, 10, 20, 21.78, 30, and 40 t/hm²). The results showed that:Compared with the control treatment, soil C stock decreased by 8.78%~15.72% in the saline soils as a result of the decrease in soil organic C stock. In contrast, soil C stock increased by 5.00%~23.94% in sodic soils with the application of FGDG largely derived from the increase of soil inorganic C stock. The C stock of wheat biomass decreased by 23.14% in saline soils and increased by 30.44% in sodic soils. The C stock of ecosystem increased by 0.09~0.42 kg/m² in sodic soils and decreased by 0.33~0.56 kg/m² in saline soils with the application of FGDG. These changes of C stock in the saline-sodic soils ecosystems were dominantly attributed to the amount of FGDG application, soil electrical conductivity, and the changes of water holding capacity caused by the application of FGDG. In a word, our study indicated that the C stock of ecosystems decreased in saline soils and increased in sodic soils, especially at the amount of 30 and 40 t/hm² FGDG. This study will provide a scientific reference for increasing soil C sequestration in arid areas.