Allotetraploidization between A and S (closely related to B) genome species led to the speciation of allotetraploid wheat (genome BBAA). However, the immediate metabolic outcomes and adaptive changes caused by the allotetraploidization event are poorly understood. Here, we investigated how allotetraploidization affected salinity tolerance using a synthetic allotetraploid wheat line (genome S S AA, labeled as 4x), its (genome S S , labeled as S S ) and (AA genome, labeled as AA) parents. We found that the degree of salinity tolerance of 4x was similar to its S S parent, and both were substantially more tolerant to salinity stress than AA. This suggests that the S S subgenome exerts a dominant effect for this trait in 4x. Compared with S S and 4x, the salinity-stressed AA plants did not accumulate a higher concentration of Na in leaves, but showed severe membrane peroxidation and accumulated a higher concentration of ROS (H O and O ) and a lesser concentration of flavonoids, indicating that ROS metabolism plays a key role in saline sensitivity. Exogenous flavonoid application to roots of AA plants significantly relieved salinity-caused injury. Our results suggest that the higher accumulation of flavonoids in S S may contribute to ROS scavenging and salinity tolerance, and these physiological properties were stably inherited by the nascent allotetraploid S S AA.