<p>Nitrogen is an essential nutrient, which plays an important role in plant growth and development process and increases crop production. However, excessive nitrogen application will lead to a series of problems such as water eutrophication and economic costs. Therefore, it is of great significance to explore rice low-nitrogen tolerance genes and breed new varieties with higher nitrogen utilization efficiency for improving the economic benefits and agricultural sustainability of agricultural production. In this study, 295 <i>japonica</i> rice varieties were used as materials to measure root dry weight, leaf dry weight and root-shoot ratio at seedling stage under low and high nitrogen conditions. By using Genome-wide association analysis and haplotype analysis of 587 genes among the 47 QTLs obtained, we finally identified significant phenotypic differences between the different haplotypes of the 96 genes. Based on the criteria of |log₂FC| &gt; 1 and <i>p</i> &lt; 0.05, 5 genes (<i>Os06g0538400</i>, <i>Os11g0195500</i>, <i>Os11g0213700</i>, <i>Os11g0213800</i>, <i>Os12g0472800</i>) were significantly different in the expression of Longjing 31 (low-nitrogen tolerant variety), but not in Songjing 10 (low-nitrogen sensitive variety), and they were named the more valuable candidate genes for low-nitrogen tolerance. <i>Os11g0213700</i> and <i>Os11g0213800</i>, as genes containing LRR structure, may regulate root development and low nitrogen stress response by interacting with <i>KAI2</i>. Mining low-nitrogen tolerance genes in rice is of great significance to rice growth and agricultural development. The results of this study provide an important molecular basis for identifying low-nitrogen tolerance genes and breeding low-nitrogen tolerant rice varieties.</p>