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Fruit yield is the most important horticultural trait of tomato. SlMBP21,a SEPALLATA subclass MADS-box gene has been reported to have functions in regulating pedicel abscission zone identity and development and controlling sepal size in tomato. However, we generated transgenic tomato plants which overexpress SlMBP21and found the transformants displayed curly leaves, abnormally shaped flowers with twisted and opened stamens, reduced yield parameters, and small and light seeds. Our studies on the gain-of-function phenotype and gene expression level showed that its novel aspects played important roles in determining leaf morphology, flower and inflorescence architecture, and seed size, as well as the fruit yield. Overexpression of SlMBP21in tomato resulted in curly leaves with fewer leaflets due to the regulation of the critical leaf polarity genes that cause an imbalance between the midvein adaxial–abaxial cell growth. Defects in the architecture of flowers and inflorescences resulted in reduced fruit set. Furthermore, we demonstrated that SlMBP21plays its role through inhibiting the expression of the genes involved in the determination of seed development in tomato and SlMBP21 protein can interact with other MADS-box protein (SlAGL11, TAGL1 and SlMBP3) to control seed size. Thus, these results suggest that overexpression of SlMBP21causes multiple types of damage to plant growth and development, especially fruit yield, in tomato.