Aim <p>Nitrogen fertilization is frequently used to modulate and enhance plant tolerance to abiotic stresses. This study aimed to investigate the effects of nitrogen fertilization on the recovery growth of maize (<i>Zea mays</i> L.) roots and its correlations with grain yield and nitrogen use efficiency after waterlogging stress.</p> Methods <p>A 2-year experiment was conducted to examine the effects of nitrogen fertilizer application rates (0, 90, 180, 270, and 360&#xa0;kg N ha^–1, designated as N1, N2, N3, N4, and N5, respectively) on root morphological and physiological characteristics under well-watered (W1) treatments throughout the maize growing season and under waterlogging for 6&#xa0;days in the sixth-leaf (V6) growth stage (W2).</p> Results <p>Compared with W1, W2 significantly decreased root length, dry weight, surface area, volume, oxidation activity, zeatin + zeatin riboside, and indole-3-acetic acid contents in the tasseling, filling, and maturity stages, regardless of nitrogen rate. Furthermore, these parameters increased with increasing nitrogen rate (up to N5) under W2, indicating that a high nitrogen rate (e.g., under N5 treatment) could enhance root recovery growth of maize after early (V6)-stage waterlogging. Moreover, N5 led to a more developed root system, contributing to improved nitrogen use efficiency under W2.</p> Conclusions <p>Collectively, a high nitrogen rate (360&#xa0;kg N ha^–1) promoted root recovery growth after waterlogging in the V6 stage, resulting in relatively high grain yield and nitrogen use efficiency in maize. These findings also provide a scientific basis for nitrogen management strategies to improve maize yield and nitrogen use efficiency under waterlogging conditions.</p>