Saline-alkaline stress is a main abiotic factor that severely limits crop growth, posing a threat to global agricultural production and food security. According to research by the Food and Agriculture Organization, over 1 billion hectares of land are affected by salt, with approximately 60% of this area experiencing alkaline salt impact. Rapid cultivation of saline-alkaline tolerant crops through molecular design breeding has emerged as a crucial strategy for utilizing and improving saline-alkaline land. However, there remains a lack of saline-alkaline tolerance genes with substantial breeding potential. Existing studies predominantly focus on plant responses to neutral salt stress, while the mechanisms underlying alkaline salt stress (referred to as “alkaline stress” hereafter) remain poorly understood. Roots serve as the frontline tissues directly encountering and perceiving saline-alkaline stress in plants. Maintaining homeostasis in the root apical meristem is critical for root growth, development, and stress adaptation. However, the gene regulatory mechanisms governing the root apical meristem's response to alkaline stress remain elusive. Our previous work found that Sesbania cannabina, a leguminous plant, is extremely alkali tolerance. S. cannabina can grow in soda saline-alkaline soil with a pH exceeding 9.5. Despite this resilience, the specific mechanisms underlying its alkali tolerance merit further exploration. We analyzed the critical time points during the alkaline stress response in S. cannabina root tips by bulk RNA-seq. Additionally, we performed single-nucleus RNA-seq to investigate how different cell types respond to alkaline stress. These comprehensive analyses lay the foundation for identifying cell-type-specific alkali-responsive genes with substantial breeding potential.