Soil salinization is one of the major limiting factors for the sustainable development of agriculture in the arid northwest China. Among them, flue gas desulfurization (FGD) gypsum from the coal-fired power plant can be widely used to improve the saline-sodic soil. At the same time, the lignite bioorganic fertilizer (LBF) has also been expected as an effective amendment for the better saline-sodic soil in recent years. However, little is known about the combined application of LBF and FGD gypsum on the physical and chemical properties of saline-sodic soil and sunflower growth. In this study, a two-year field experiment was conducted in 2021-2022, in order to investigate the effect of combining both LBF and FGD gypsum on the saline-sodic soil quality, crop yield, water use efficiency (WUE), and partial-factor productivity of N (PFPn) in the sunflower farmland at the Hetao Experimental Station of China Agricultural University, located in the Bayannur City, Inner Mongolia Autonomous Region, China. Soil samples of 0-40 cm soil layer were collected at the sunflower maturity stage. The sunflower yield, WUE, and PFPn were measured at the same time. Six treatments were considered, i.e., a chemical fertilizer treatment (CK), and 2 t/hm² LBF combined with 0 (LBF), 5 (LBF+F5), 10 (LBF+F10), 15 (LBF+F15), and 20 (LBF+F20) t/hm² FGD gypsum application treatments. The results showed that the LBF treatment decreased the average content of Na⁺ by 23.33% in the 0-40 cm soil layer in 2022, compared with the CK treatment, but there was no effect on the other water-soluble ions. The LBF+F20 treatment increased the average contents of Ca²⁺, SO₄^2- and Mg²⁺ by 450.71%, 123.41%, and 391.90%, respectively, compared with the CK, whereas, there was the a decrease in the average contents of CO₃^2-+HCO₃^- by 48.29% in 0-40 soil layer. The LBF combined with the FGD gypsum treatments significantly decreased the average soil pH by 0.29-0.88 in the 0-20 cm soil layer. The soil organic matter content in the 0-20 cm soil layer was higher than that in the 20-40 cm soil layer. The LBF treatment significantly increased the soil organic matter content by 39.89%-131.65% in the 0-20 soil layer in 2021-2022. In addition, the LBF combined with FGD gypsum treatments decreased the soil ESP and soil bulk density by 18.34%-43.42%, and 5.91%-11.06% in the 0-40 cm soil layer, respectively, compared with the CK. The LBF+F10, LBF+F15, and LBF+F20 treatments increased the soil aggregate mean weight diameter by 102.00%, 127.78%, and 91.95%, respectively, but there was no effect on the soil percentage aggregate destruction. Although the application of FGD gypsum decreased the soil pH and ESP, however, the excessive application of FGD gypsum would increase the soil salt content, which may inhibit the sunflower growth and yield improvement. The LBF+F10 treatment increased the sunflower yield, WUE, and PFPn by 44.45%, 44.62%, and 80.46%, respectively, compared with the CK. In general, the combination of 2 t/hm² LBF and 10 t/hm²FGD gypsum shared the greatest effect on the physical and chemical properties of saline-sodic soil, indicating the largest sunflower yield, WUE, and PFPn. The finding can provide the scientific implication for the saline-sodic soil remediation and crop productivity improvement of salinized farmland in HID.