Waterlogging (WL) during the early growing stage is one of the most important environmental factors limiting maize (Zea mays L.) production. The application of nitrogen (N) fertilizer is important to maintain normal plant growth and defense against abiotic stresses. However, the effects of N fertilization on biomass accumulation and partitioning, as well as N utilization in maize under WL stress remains unclear. Thus, we conducted a two-year field experiment at Jingzhou City, Central China to investigate the effects of varying N fertilizer application rates (0, 90, 180, 270, and 360 kg N ha⁻¹) on shoot biomass accumulation and its distribution, N uptake, and N use efficiency in maize under well-watered (WW) conditions throughout the maize growing season and WL for 6 d at the sixth leaf stage. Compared to the WW condition, WL significantly reduced shoot biomass, N accumulation, harvest index, N harvest index, nitrate reductase activity, N use efficiency, and N partial factor productivity at all N application rates. Moreover, these parameters (excluding N partial factor productivity) increased with increasing N application rates (up to 360 kg N ha⁻¹) under WL, suggesting that a high N rate (such as 360 kg N ha⁻¹) could improve the accumulation and distribution of shoot biomass and N utilization of waterlogged maize. The enhanced shoot biomass, nitrate reductase activity, N accumulation, and N use efficiency were related to increased root biomass and root length density at higher N treatments under WL. In addition, compared with other N treatments, 360 kg N ha⁻¹ resulted in a better proportion of biomass distribution in the kernel and improved transfer of biomass from the vegetative organs to grain under WL, which accounted for the enhanced harvest index. Therefore, an appropriate increase in the nitrogen application rates (up to 360 kg N ha⁻¹) helped to improve biomass accumulation in the shoot and its transfer to the grain, together with N use efficiency in maize under early (sixth leaf)-stage waterlogging.