Abstract: Inappropriate irrigation and fertilization have led to high carbon (C) emissions and degradation of ecosystem services in the saline-alkali sunflower farmland in the arid upper Yellow River basin of Northwest China. This study aims to determine the rational irrigation and fertilization strategy for the sustainable production of saline-alkali sunflower farmland in this area. A field experiment was carried out to investigate the effects of organic fertilizer application on the net ecosystem carbon budget (NECB) and ecosystem service values of saline-alkali farmland under drip irrigation in 2021 and 2022. Two factors were considered, including the lower limit of irrigation and the fertilization mode. Among them, the lower limit of irrigation (drip irrigation) was divided into two soil matric potential thresholds (SMPT) (W1: −20 kPa SMPT and W2: −30 kPa SMPT). Three fertilization modes were selected (CK: Chemical fertilizer, LBF: Lignite C-based organic fertilizer 4.5 t/hm², SMF: Sheep manure compost 5 t/hm²) under each SMPT using a completely random block design. In addition, the border irrigation combined with chemical fertilizer was set as the control treatment (MCK), corresponding to the local farmer practices. A comparison was performed on the NECB of different ecosystems and the components, as well as three ecosystem service values (supply function value of agricultural products, accumulated functional value of organic matter, and gas regulation value) among different treatments. Results indicated that the LBF and SMF treatments effectively promoted crop growth and biomass accumulation, compared with the CK. There was also an increase in the soil moisture content and soil organic matter (SOM) content under the drip irrigation. Among all treatments, better performance was achieved in drip irrigation with −20 kPa SMPT combined with 4.5 t/hm² lignite C-based organic fertilizer application treatment (W1LBF). The highest aboveground biomass and yield also increased by 32.30% and 44.13%, respectively, compared with the MCK. These soil and crop indicators depended mainly on the NECB. The net primary productivity (NPP) and grain C output were the main components of the carbon sink and carbon source in the farmland system, respectively. NPP, SOM content, grain C output, and soil C emission in the drip irrigation treatment were higher than those in the surface under the same fertilization, where the values of these indicators increased with the increase of SMPT. Moreover, the organic fertilizer application (LBF and SMF) also significantly improved NPP, SOM content, and grain C output under the same irrigation, but reduced the soil C emissions, compared with the chemical fertilizer application (CK). The W1LBF treatment obtained the highest NPP and lower soil C emissions, thus achieving the highest NECB. Compared with the W1CK and MCK treatments, the W1LBF treatment increased NECB by 26.24%-159.98% and 151.74%, respectively. In addition, the changes in NPP, SOM, and soil carbon emissions also significantly affected the ecosystem service value. W1LBF treatment increased the supply function value of agricultural products, SOM accumulation, and gas regulation by 8004.20, 923.90, and 2094.70 Chinese Yuan/hm², respectively, compared with the MCK. In conclusion, the drip irrigation with −20 kPa soil matric potential thresholds combined with 4.5 t/hm² lignite C-based organic fertilizer application can effectively increase the C sink and service values from the saline-alkali sunflower farmland ecosystem in the arid upper Yellow River basin of Northwest China. The research can provide the scientific basis for the saline-alkali farmland C sequestration and ecosystem service value, while greenhouse gas emission reduction in the arid and semi-arid areas.