Abstract: In this experiment, ‘Provence’ tomato was used as the test material, and a combination of root basal application and foliar-spraying of Fe, Zn, and Se fertilizers was adopted to explore the effects of combined application of these elements on fruit quality, flavor, and mineral element content in tomato. Eight treatments were set, including spraying distilled water (CK), foliar-spraying of 50 μmol(Zn)∙L⁻¹ ZnSO₄·7H₂O Zn(L), foliar-spraying of 100 μmol(Fe)∙L⁻¹ EDTA-Fe Fe(L), root application of 0.1 g(Zn)∙L⁻¹ ZnSO₄·7H₂O Zn(R), root application of 0.1 g(Zn)∙L⁻¹ ZnSO₄·7H₂O + foliar-spraying of 100 μmol(Fe)∙L⁻¹ EDTA-Fe Zn(R)+Fe(L), root application of 0.05 g(Se)∙L⁻¹ Se rich organic fertilizer Se(R), root application of 0.05 g(Se)∙L⁻¹ Se rich organic fertilizer + foliar-spraying of 50 μmol(Zn)∙L⁻¹ ZnSO₄·7H₂O Se(R)+Zn(L), and 0.05 g(Se)∙L⁻¹ Se rich organic fertilizer + foliar-spraying of 100 μmol(Fe)∙L⁻¹ EDTA-Fe Se(R)+Fe(L). Fruit weight, nutrient content, amino acid content, volatile flavor compound content, and elemental content were investigated to determine the optimal combination of Fe, Zn, and Se. The results showed that 1) both the sole and combined applications of Fe, Zn, and Se significantly increased the fruit weight of tomato in comparison to CK, with Zn(R) increasing fruit weight by 63.40% (P<0.05). 2) Zn(L) and Se(R)+Zn(L) treatments significantly increased soluble sugar and titratable acidity contents in the fruits in comparison to CK, with soluble sugar and titratable acidity significantly increasing by 63.88% and 55.17% (P<0.05) under Se(R)+Zn(L) treatment. 3) The Se(R)+Zn(L) treatment significantly increased the content of essential amino acids, such as valine and phenylalanine, and five non-essential amino acids, such as serine, aspartic acid, and glutamic acid, in comparison to CK. 4) Zn(R)+Fe(L), Se(R)+Zn(L), and Se(R)+Fe(L) increased the content of aroma compounds in tomato fruits and improved the flavor quality of the crop in the order of Zn(R)+Fe(L) > Se(R)+Zn(L) > Se(R)+Fe(L). 5) Compared with CK, the sole and combined applications of Fe, Zn, and Se could increase the contents of major elements and microelements in tomato fruits in most cases. The Ca content significantly increased by 110.00% under both Zn(L) and Fe(L) treatments. Similarly, Mn content significantly increased by 73.86% and 121.16%, respectively (P<0.05). The Mn content under Se(R) and Se(R)+Zn(L) treatments significantly increased by 350.62% and 307.88%, respectively (P<0.05). 6) Principal component analysis of tomato fruit growth and quality indices showed that the Zn(R)+Fe(L) and Se(R)+Zn(L) treatments demonstrated higher composite values, indicating that these treatments had the most notable impact on enhancing the nutritional quality of tomato fruits.