Agricultural wastes have the potential to enhance the utilization rate and production efficiency in saline-alkali land. In this study, humic acid was incorporated into a substrate module composed of agricultural wastes, including wine lees and straw. A series of experiments was conducted to investigate the effects of various substrates on soil salinity in saline-alkali environments. The "Jinpeng 8 Type B" tomato served as the test sample. Three types of saline-alkali soils were selected: mild S1 (Ec = 1.15 mS/cm, pH = 8.63), moderate S2 (Ec = 3.67 mS/cm, pH = 9.13), and heavy S3 (Ec = 6.39 mS/cm, pH = 9.69). Six groups of humic acid additions were established: T0 (0), T1 (2‰), T2 (4‰), T3 (6‰), T4 (8‰), and T5 (10‰), with the treatment lacking humic acid serving as the control group. The analytic hierarchy process (AHP) and entropy weight methods were employed to assign subjective and objective weights to each indicator. The final weights for each indicator related to tomato cultivation were derived from this assignment. A TOPSIS multi-objective comprehensive evaluation model was constructed, incorporating 16 indicators across three categories: tomato growth physiological indicators, yield, and fruit quality. This model facilitated the determination of optimal substrate allocation for the different types of saline-alkali soils. The results indicated a trend of increasing and then decreasing soil salinity across different types of saline-alkaline soils during the tomato growth stages, from seedling to flowering, fruit enlargement, and maturity. The salt content exhibited a similar trend of increasing and then decreasing with increasing soil layer depth. At the same depth, soil salinity decreased with the addition of humic acid to the substrate. The average salt contents of each soil layer for mild, moderate, and heavy saline-alkali soils treated with 10‰ humic acid were reduced by 60.57%, 13.14%, and 8.31%, respectively, compared to the control group. Notably, the addition of humic acid was most effective in improving mild saline-alkali soil conditions. The humic acid treatment significantly enhanced plant height, stem diameter, soil and plant analyzer development (SPAD), root characteristics, yield, and quality of tomatoes (P<0.05). The parameters for tomato plant height, stem diameter, SPAD value, and root characteristics exhibited a trend of increasing and then decreasing with higher amounts of humic acid added. An optimal combination was identified for evaluating tomato plant height, stem diameter, SPAD value, root characteristics, yield, and quality. In comparison to the absence of humic acid, the addition of 4‰, 6‰, and 8‰ humic acid in mild, moderate, and heavy saline-alkali soils, respectively, resulted in corresponding increases in root quality of 51.17%, 49.60%, and 56.98%, indicating a well-developed root system. The comprehensive indexes for tomatoes were 0.9030, 0.8934 and 0.8304 in mild, moderate, and heavy saline-alkali soils with 4‰, 6‰, and 8‰ humic acid, respectively. These findings provide a theoretical basis for the efficient utilization of agricultural waste and the scientific management of high-quality fruit and vegetable production in saline-alkali land.