Between the two major rice subspecies, indica varieties generally exhibit higher nitrate (NO₃^‒) uptake and nitrogen (N)-use efficiency (NUE) than japonica varieties. Introducing efficient NO₃^‒ utilization alleles from indica into japonica could improve NUE, and at the same time uncover unknown regulators of NO₃^‒ metabolism. Here, we identify OsWRKY23 as a key regulator of NO₃^‒ uptake and NUE differences between indica and japonica rice. The OsWRKY23^indica allele exhibits reduced transcriptional activation of a negative regulator of auxin accumulation, DULL NITROGEN RESPONSE1 (DNR1). The resultant increase in auxin level improves NO₃^‒ uptake and assimilation, which ultimately enhances grain yield. Geographical and evolutionary analyses reveal overlapping distribution of OsWRKY23^indica and DNR1^indica, particularly in low-fertility soils, suggesting their involvement in the adaptation to low N conditions to improve NUE and grain yield. Incorporating the OsWRKY23-DNR1 module from indica rice represents a promising strategy to enhance japonica NUE, which is crucial for sustainable agriculture.