To evaluate the effects of saline water on the yield and quality of tomatoes, a late fruit-setting stage irrigation experiment was conducted in a greenhouse using two cultivars: medium-fruited, tasty Strawberry tomato (fresh-eating) and large-fruited Maofen tomato (fresh/processing). For this, plants were grown in pots containing substrate, and five irrigation water electrical conductivity (EC) levels (1.0 as control, 2.6, 4.2, 5.8, and 7.4 dS m⁻¹) were applied for each cultivar, resulting in a 2 × 5 factorial design with 10 treatments in total. Then, tomato growth, fruit ion composition, and quality attributes were evaluated. The results showed that 1.0–7.4 dS m⁻¹ saline water had no significant impact on the plant height, stem diameter, single-fruit weight, or total yield of either cultivar. However, Strawberry tomato’s marketable yield decreased by 23.5% at 7.4 dS m⁻¹. The yield per plant of Maofen tomato was 2.7 times that of Strawberry tomato. Fruit Na⁺ content increased with EC for both cultivars; Maofen tomato had higher Na⁺ and a lower K⁺/Na⁺ ratio, with greater ion content responses to salinity. Regression analysis revealed distinctly nonlinear responses in key yield, ion, and quality parameters across the salinity gradient. The fruit comprehensive quality score (CQS) rose with EC, and Strawberry tomato’s average CQS increase (109%) was significantly higher than Maofen tomato’s. In conclusion, saline irrigation initiated when the fourth-cluster fruits attained 60% of the final harvested diameter, at EC ≤ 5.8 dS m⁻¹ for Strawberry tomato and ≤7.4 dS m⁻¹ for Maofen tomato, improved fruit quality without compromising yield. Strawberry tomato is recommended for quality-oriented production, whereas Maofen tomato is better suited for yield-oriented production, providing scientific support for saline water utilization in greenhouse soil-less cultivation.