Soil salinity is one of the major limiting factors in agricultural productivity. Desulfurization waste could be recycled to improve saline-alkaline soil, and this could provide stability in food production. In this study, desulfurization waste was applied to oil-sunflower seedlings to improve their resistance to saline-alkaline conditions. The distribution of calcium, total calcium content, and calcium ATPase (Ca²⁺-ATPase) activities in leaves cells were measured after exogenous treatment with desulfurization waste or calcium sulfate (CaSO₄). In control experiments under alkaline stress, there were few calcium precipitates in the chloroplast and vacuole, and the chloroplast structure was deformed. Calcium precipitates increased in the cell wall, intercellular space and vacuole, and the chloroplast structure remained intact after applying desulfurization gypsum or CaSO₄ to the sunflowers. The Ca²⁺-ATPase activities in the plasma membrane and tonoplast increased with the desulfurization waste or CaSO₄ dose, and activity was higher in the tonoplast than in the plasma membrane. The total calcium content also increased with the treatment dose. Both desulfurization waste and CaSO₄ contributed to calcium influx into the cell through the plasma membrane and tonoplast, which maintained the stability and integrity of the membrane and cell wall structure and reduced injury to the sunflower under alkaline stress.