In order to clarify the effects of balanced fertilization on tomato cultivated in substrate in the greenhouse, the tomato (Solanum lycopersicum L.) cultivar 184 was used as test material. Four treatments were designed according to the principle of balanced fertilization of N, P and K, namely no fertilization (CK0), conventional fertilization (CK, 23.7 kg N, 38.4 kg P2O5 and 72.9 kg K2O per 667 m2), balanced fertilization 1 (T1, 38.38 kg N, 16.45 kg P2O5 and 53.18 kg K2O per 667 m2), balanced fertilization 2 (T2, 10% less fertilizer than T1, 33.58 kg N, 514.4 kg P2O, 46.5 kg K2O per 667 m2), effects of balanced fertilization on tomato growth, quality, yield and mineral element content were studied. The results showed that balanced fertilization could promote tomato growth, improve quality, mineral element content and yield in different degrees, balanced fertilization 1 (T1) had the best effect. Compared with CK, plant height, leaf number, maximum net photosynthetic rate and root activity of tomato in T1 treatment increased by 9.97%, 5.19%, 25.13% and 95.79% respectively; soluble solid, soluble sugar, iron, magnesium, calcium and yield in T1 treatment increased by 19.82%, 16.09%, 15.24%, 11.30%, 69.06% and 15.25%, respectively. The results of correlation and principal component analysis showed that there was a certain correlation and dependence between the quality and yield of tomato indexes. According to the final comprehensive score model, it was found that the score of T1 treatment was the highest and CK0 was the lowest, indicating that balanced fertilization had a great impact on the growth, quality, mineral elements contents and yield of tomato cultivated in substrate. Among them, the fresh weight of single fruit and contents of VC, mineral elements, phosphorus, potassium, iron, manganese and zinc were the main factors affecting the growth and quality of tomato. Therefore, the balanced fertilization 1 treatment (T1) could be a fertilizer application pattern for rational allocation of fertilizer resources by enhancing the photosynthetic capacity of tomato leaves, increasing yield and improving fruit quality.