In order to screen the optimal combination of functional fertilizers for increasing yield and improving quality in the production of substrate-grown cherry tomatoes, cherry tomato ‘Fragrant Feminine 9’ was used as the material, and seven different combinations of functional fertilizers were set up, including blank control (CK), amino acid (T1), potassium xanthate (T2), alginate (T3), amino acid+potassium xanthate (T4), amino acid+alginate (T5), and potassium xanthate+alginate (T6). The functional fertilizers and nutrient solution were applied by drip irrigation to study the effects of different functional fertilizers on quality, yield and substrate environment of substrate-grown cherry tomatoes. The results showed that compared with CK, the addition of alginate (T3) obviously increased the net photosynthetic rate, intercellular CO2 concentration and yield of cherry tomatoes by 39.97%, 6.61% and 22.32%, respectively. The combination of T4 and T5 functional fertilizers not only significantly increased microbial quantities, and the activities of urease, sucrase, alkaline phosphatase and catalase in the substrate, but also significantly improved the quality and yield of cherry tomatoes, with a yield increase by 20.16% and 12.84%, respectively. It was found that the T5 treatment performed the best by comprehensive evaluation. In conclusion, the substrate environment can be improved, and the fruit quality and yield can be increased by adding 50 mg/L amino acids and 5 mg/L alginate in the nutrient solution to cultivate cherry tomatoes using drip irrigation.