The objectives were to investigate the underlying mechanisms of ammonium (NH4 ) toxicity and analyse the attenuation of NH4 toxicity by nitrate (NO3−) in wheat. Experiments were performed with three treatments, including wheat seedlings grown with 7.5 mM NO3− (control), 7.5 mM NH4 (HA), or 7.5 mM NH4 plus 1 mM NO3− (AN). The HA treatment led to increased NH4 content, severe growth retardation, and decreased root biomass compared to the control. AN improved root growth but did not decrease the root NH4 content. HA generally upregulated the expression of several kinds of ATPases, including the AAA-ATPase family associated with various cellular activities, calcium-transporting ATPases, vacuolar-type H -transporting ATPases, and ABC transporters, while genes encoding ATP synthesis enzymes were downregulated. The NO3−-dependent attenuation was accompanied by decreases in the transcription of genes encoding these ATPases and increases in that of genes associated with ATP synthesis in the roots. Physiological determination showed that HA enhanced Ca2 -Mg2 -ATPase activity and decreased the ATP content in the roots, while AN attenuated these changes. The results of functional enrichment analyses and physiological determination were highly consistent with the expression patterns of genes encoding ATP-associated proteins. In conclusion, some metabolic pathways were altered by NH4 nutrition alone, thus leading to energy overconsumption as well as root growth inhibition; NO3− alleviates NH4 toxicity by improving ATP synthesis and overuse in the roots of wheat seedlings.