Soil degradation and water scarcity are major constraints for agriculture in arid and semi-arid regions. Yellow sand substrates, characterized by low cation exchange capacity, high permeability, and poor water and nutrient retention, have significant potential for use in agricultural facilities in arid regions, such as southern Xinjiang. However, the mechanisms by which yellow sand substrates affect crop photosynthetic performance, dry matter accumulation, and yield throughout the growth cycle remain poorly understood. To address this gap, a two-year (2023-2024) solar greenhouse experiment was conducted with four irrigation levels (I1: 100 % ETc, I2: 85 % ETc, I3: 70 % ETc, I4: 55 % ETc) and three fertilization rates (F1: 120 % F0, F2: 100 % F0, F3: 80 % F0) to analyze the responses of tomato growth, photosynthesis, and yield under different water-fertilizer regimes in yellow sand substrates. A multi-objective evaluation framework was applied, combining a Nash equilibrium-based integration of subjective and objective weighting with an improved TOPSIS method incorporating a virtual ideal solution to comprehensively assess seven key indicators, including growth, photosynthesis, and yield. The results showed that irrigation and fertilization significantly affected root dry weight at the seedling stage(S-RDW), leaf dry weight at the flowering and fruiting stages(F-LDW), fruit dry matter (FDM) content, chlorophyll content at the flowering and fruiting stages(F-CHl), and net photosynthetic rate at the seedling stage(S-Pn). Pearson's correlation analysis identified seven phenotypic indicators significantly correlated with yield (Y). Path analysis further revealed that FDM had the strongest direct effect on Y, followed by RDW, at the seedling stage. Moderate deficit irrigation (70-85 % ETc) combined with medium-to-high fertilization (100-120 % F0) significantly increased yield and water use efficiency (WUE). Under cultivation with a yellow sand substrate, this water-fertilizer combination optimally enhanced photosynthetic performance, promoted dry matter accumulation, and stabilized yield, thereby enabling both water savings and increased yield. These findings offer a theoretical foundation and technical guidance for the development of water-efficient, high-yield, and sustainable facility agriculture in the Gobi Desert and other arid regions.