Tomato (Solanum lycopersicum L.) is an important vegetable crop around the world, and water scarcity and soil salinization are two major unfavorable factors limiting the fruit yield and quality of greenhouse tomato in arid and semi-arid regions. The application of exogenous silicon has been reported to enhance tomato yield under salt or drought stress, but its effect under combined salt-drought stress remains unclear. A two-season (autumn 2021 and spring 2022) experiment was conducted with three irrigation levels (I1, 90%−100% θf, where θf is the field capacity; I2, 70%−80% θf; I3, 50%−60% θf), two soil salinity levels (S0, 0.1%, g/g; S1, 0.4%, g/g) and two silicon application rates (T0, 0 mM; T1, 2.4 mM) to explore their combined effects on leaf silicon content, photosynthetic parameters, fruit yield, nutrient yield, crop water productivity (WP), nitrogen uptake and utilization, nutrient water productivity (NWP) and economic benefit of drip-irrigated greenhouse tomato. The results showed that deficit irrigation and salt stress exerted significant inhibiting effects on leaf silicon content, photosynthetic parameters, tomato yield, and water-nitrogen productivity, but the inhibition was alleviated by silicon application, which increased leaf silicon content by 67.0%, net photosynthetic rate (Pn) by 25.3%, fruit yield by 12.3%, WP by 11.9%, nutrient yield by 10.0% (titratable acids) - 27.4% (soluble sugars) and NWP by 9.2% (titratable acids) - 26.1% (soluble sugars) on average. The average fruit yield over the two growing seasons was 66.01, 54.29 and 44.31 t ha−1 under I1, I2 and I3, and the silicon application increased average leaf silicon content by 71.9%, 65.2% and 63.0%, Pn by 11.1%, 12.9% and 7.6%, and fruit yield by 12.8%, 16.2%, and 8.1% at the three irrigation levels, respectively. Plant nitrogen uptake (NU) and nitrogen partial factor productivity (NPFP) increased but nitrogen use efficiency (NUE) tended to decrease with the increasing irrigation level, while silicon application improved NUE by 3.9% and 2.2% and NPFP by 13.8% and 11.7% in the two growing seasons, respectively. Silicon application significantly increased net profit by 24.3% and 17.7% in autumn 2021 and spring 2022, respectively. According to the principal component analysis, I1T1S0 ranked first in both growing seasons. The correlation matrix showed that fruit yield was positively correlated with leaf silicon content, Pn, stomatal conductance, WP, NU, NUE, NPFP, nutrient yield and net profit, while it had negative correlation with NWP. In conclusion, exogenous silicon application can improve the fruit yield and nutrient yield of drip-irrigated greenhouse tomato by enhancing leaf silicon content and photosynthetic capability under drought-stressed and salt-affected conditions.