The absorption and utilization of NH₄⁺ and NO₃⁻ by plant roots is closely related to soil moisture. In this study, we investigated the effect of short-time drought and rewatering on uptake and assimilation of NH₄⁺ and NO₃⁻ in 1-year-old Malus hupehensis plants, as well as transcription changes of ammonium transporters (AMTs) and nitrate transporters (NRTs). In roots, the NH₄⁺ and NO₃⁻ content and nitrate reductase activity decreased under drought and to some extent was restored after rewatering. Expression analysis indicated that most investigated AMTs and NRTs were down-regulated while MhAMT1;2 was significantly up-regulated in drought-stressed roots. Therefore, the function of MhAMT1;2 was further studied through bioinformatics analysis, tissue-specific expression, subcellular localization, and functional complementation in NH₄⁺ uptake-defective yeast and Arabidopsis mutants. Results showed that MhAMT1;2 was mainly expressed in roots and localized to the cell membrane. Moreover, MhAMT1;2 can mediate NH₄⁺ uptake in both yeast and Arabidopsis mutants, and the transport process was affected by external proton concentrations and ATP. The present study will create a basis for exploring the functional roles of plant AMT members and improving N uptake and use efficiency under drought condition in fruit trees.