Wind-disturbance is a potential eco-friendly technique for tackling leggy seedlings. This study uses orthogonal experimental design and seedlings vigour assessment by strong seedling index (SSI) to investigate winddisturbance on regulating tomato seedlings growth. Changes in endogenous hormone levels and biomechanical properties of tomato seedlings were investigated using enzyme-linked immunosorbent assay and uniaxial tension tests. Results showed that factors influencing significantly SSI, in descending order, are wind disturbance time (T), seedling age at the onset of wind disturbance (SA), wind velocity (V), and interval time (I). The winddisturbance effect was found to be optimal with SSI = 0.126 for a condition where V, T, I and SA values are 3 m s− 1, 1 min, 30 min, and 15 days, respectively. V and T were positively correlated with the ethylene and abscisic acid content in seedling leaves, abscisic acid and auxin content in stems, cytokinin and ethylene content in roots, and the elastic moduli of stems and roots but negatively associated with the cytokinin content in stems and leaves, auxin and abscisic acid content in roots, and leaves’ elastic modulus. Wind disturbance mechanism for controlling seedlings growth involved eliciting the accumulation of abscisic acid in stems and leaves and reduction of the auxin content in roots to about the optimal threshold for roots growth thereby reducing seedling stems and leaves development and promoting a better roots growth and a high SSI. This work offers theoretical insights and technical guidance for utilising wind-disturbance as a sustainable seedling  and personalised seedling management approach.