A larger root system enhanced biomass accumulation, and high nitrogen (N) metabolism is an effective mechanism of plants in response to low N stress. How cotton plants balance N metabolism and enhanced biomass accumulation to support larger root systems under low N stress remains to be elucidated. This study deals with the changes in root development due to biomass accumulation and N metabolism in contrasting N‐efficient cotton genotypes (CCRI‐69, N‐efficient, and XLZ‐30, N‐inefficient) under low (0.2 mM) and normal (2 mM) N concentrations. The results showed that genotype CCRI‐69 produced a larger root system, high biomass accumulation, and N metabolism than XLZ‐30. The flourishing root system of CCRI‐69 was due to more allocation of sugars from shoot to root, especially under low N concentrations, to support efficient N uptake followed by high N metabolism and N use efficiency (NUE). In addition, CCRI‐69 produced more dry biomass, high photosynthetic activity, N‐related enzymatic activities, N uptake, and utilization under normal N concentration compared with XLZ‐30. Based on multivariate analysis, root morphological traits, sugar contents, and N‐assimilating enzymatic activities might be considered the key traits contributing to NUE and can also be used as potential indicators for genotypic evaluation. In the future, high N metabolism and allocation of more sugars under low N concentration could be studied at a molecular level to better understand the underlying molecular mechanism of NUE in cotton.