Root system architecture (RSA) plays a critical role in the acquisition of water and mineral nutrients. In order to understand the root characteristics that contribute to enhanced crop yield and N accumulation high-yielding and N efficient cultivars under N-stressed conditions. Here, grain yield, N accumulation and RSA traits of six dominant maize cultivars (CD30, ZH311, ZHg505, CD189, QY9 and RY1210) grown in the Southwestern part of China were investigated in field experiment under three different N regimes in 2019–2020; N300 (300 kg N ha−1), N150 (150 kg N ha−1) and N0 (no N supplied). Using Root Estimator for Shovelomics Traits (REST) for the quantitative analysis of maize root image obtained in the field, RSA traits including total root length (RL), root surface area (RA), root angle opening (RO), and root maximal width (RMW) were quantified in this study. The results showed that Yield, N accumulation and RSA were significantly affected by N rates, cultivars and their interactions. Grain yield, N accumulation and root weight showed a similar trend under N300 and N150 conditions compared to N0 conditions. With the input of N fertilizer, the root length, surface area, and angle increase, but root width does not increase. Under the N300 and N150 condition, RL, RA, RO and RMW increased by 17.96%, 17.74%, 18.27%, 9.22%, and20.39%, 18.58%, 19.92%, 16.79%, respectively, compared to N0 condition. CD30, ZH505 and RY1210 have similar RO and RMW, larger than other cultivars. However, ZH505 and RY1210 have 13.22% and 19.99% longer RL, and 11.41% and 5.17% larger RA than CD30. Additionally, the grain yield of ZH505 and RY1210 is 17.57% and 13.97% higher compared with CD30. The N accumulation of ZH505 and RY1210 also shows 4.55% and 9.60% higher than CD30. Correlation analysis shows that RL, RA, RO and RMW have a significant positive correlation with grain yield while RO and RMW have a significant positive correlation with N accumulation. Linear plus plateau model analysis revealed that when the RO reaches 99.53°, and the RMW reaches 15.18 cm, the N accumulation reaches its maximum value under 0–300 kg N ha−1 conditions. Therefore, selecting maize cultivars with efficient RSA suitable for different soil N inputs can achieve higher grain yield and N use efficiency.