Purpose Seed orientation is widely known to affect shoot growth, but the effects on root growth and crop drought tolerance are unclear. Thus, one germination paper experiment, two soil pot experiments and one field experiment were conducted to study the effects of seed orientation (Brush-up, Brush-down, Crease-up and Crease-down) on crop root and shoot growth under two water treatment levels (full and deficit) using winter wheat (Triticum aestivum L.) as an example. Methods Seedling root traits, early shoot growth, mature root distribution, soil water consumption, root/shoot ratio, harvest index and grain yield were measured. Results The results showed that under full irrigation, the control Brush-up orientation allowed for the highest grain production, mainly due to shoot growth. However, Crease-down resulted in the highest yield under limited-water supplies because root biomass was optimally related to grain yield in the pots, and a reasonably deep root system (lower root biomass and longer specific root length) benefitted yield production in the field. The higher shoot biomass, lower root/shoot ratio and higher harvest index also contributed to a higher grain yield under deficit irrigation, suggesting that sowing seeds lying flat with the crease down can optimize root and shoot growth and improve drought tolerance. Conclusions To our knowledge, this is the first report verifying that seed orientation can significantly regulate root growth under dry conditions, providing a possible new mechanism underlying crop drought tolerance.