Ammonium toxicity in plants is considered a global phenomenon, but the primary mechanisms remain poorly characterized. Here, we show that although the addition of potassium or nitrate partially alleviated the inhibition of rice seedling root growth caused by ammonium toxicity, the combination of potassium and nitrate clearly improved the alleviation, probably via some synergistic mechanisms. The combined treatment with potassium and nitrate led to significantly improved alleviation effects on root biomass, root length, and embryonic crown root number. The aberrant cell morphology and the rhizosphere acidification level caused by ammonium toxicity, recovered only by the combined treatment. RNA sequencing analysis and weighted gene correlation network analysis (WGCNA) revealed that the transcriptional response generated from the combined treatment involved cellulose synthesis, auxin, and gibberellin metabolism. Our results point out that potassium and nitrate combined treatment effectively promotes cell wall formation in rice, and thus, effectively alleviates ammonium toxicity.