Freshwater shortage is common in most areas of the world, especially in arid and semiarid regions. Although saline water can be an alternative to freshwater in agricultural production, continuous saline (NaCl) water irrigation can easily lead to adverse effects on the soil-crop system. In this study, we measured the effects of flue gas desulfurization (FGD) gypsum, straw compost (SC), the SC mixed with FGD gypsum on site and the SC co-composted with FGD gypsum on soil properties, root nutrient uptake, shoot growth, crop yields and tomato quality under continuous saline water irrigation. The treatments considered were (i) untreated soils irrigated with non-saline water (control), (ii) untreated soils irrigated with saline water (SW), (iii) soils treated with SC and irrigated with saline water (SW + C), (iv) soils treated with FGD gypsum and irrigated with saline water (SW + G), (v) soils treated with the SC mixed with FGD gypsum on site and irrigated with saline water (SW + C+G), and (vi) soils treated with co-composted FGD gypsum-SC and irrigated with saline water (SW + GC). In general, under untreated soil conditions, continuous saline water irrigation resulted in adverse effects on soil properties (e.g. enhanced Na+ and sodium adsorption ratio and reduced nutrient availability) and tomato growth (e.g. the reduction of photosynthesis rate, plant growth rate, plant biomass and fruit yield, and the enhancement of blossom-end rot in tomato fruit). However, these adverse effects of continuous saline water irrigation were efficiently alleviated by the application of FGD gypsum and/or SC. The application of co-composted FGD gypsum-SC resulted in the highest fruit yield and the lowest blossom-end rot under continuous saline water irrigation. Plant straw co-composted with FGD gypsum can improve soil properties, maintain crop yields and enhance fruit quality under continuous saline water irrigation.