In recent years, the widespread application of growth regulators and nutrients to boost yield and quality of strawberry fruits has led to the rapid growth of strawberry industry globally. Although the effects of major nutrients on strawberry yield have been widely studied, investigations into the effect of trace elements such as boron remain limited. This study examined the effect of boron application on the yield and quality of “Benihoppe” strawberry fruits. Nutrient solutions with varying boron concentrations (0, 0.024, 0.048, 0.072, and 0.096 mM) were applied to the plants, and their effect on fruit quality was evaluated. The results indicated that boron application enhanced the yield per plant, nutrient composition (total amino acid and vitamin C content), antioxidant properties (total phenol) and volatile components (esters) in strawberry fruits. Specifically, treatment with 0.048 mM boron concentration significantly increased the accumulation of soluble sugars, such as sucrose, whose concentration was 154.29% higher than that of the control treated with 0 mM concentration. This enhancement is attributable to the regulated expression of sucrose phosphate synthase (maker-Fvb2-2-augustus-gene-229.38) and β-fructofuranosidase-1/2/3 (augustus-masked-Fvb5-4-processed-gene-2.0, maker-Fvb5-3-augustus-gene-272.30, and maker-Fvb5-1-augustus-gene-0.37) genes, which play crucial roles in sugar metabolism and enzyme activity. Overall, boron application enhanced the quality of “Benihoppe” strawberries. The findings of this study offer substantial theoretical and practical guidance for using boron fertilizers in strawberry farming.