Understanding the regime shifts of social-ecological systems (SES) and their local and spillover effects over time is crucial for ensuring future sustainability. However, limited research has focused on regime changes in SES under different modes of water resource utilization. In this study, we employ a concise theoretical framework to analyze regime shifts in the arid Tarim River Basin, considering changes in SES components. Additionally, we explore the drivers and local and regional effects of these shifts. The regime shifts in SES are categorized into four evolutionary phases: “Low productivity,” “Slow population expansion,” “Rapid environmental destruction,” and “Ecological restoration and improvement” over the past 12,000 years. The reciprocal coupling of SES components plays a vital role in determining the regime of SES, which is heavily influenced by the utilization of water resources and the degradation of the environment. While increasing water consumption is a core factor leading to environmental destruction, it also drives socioeconomic growth. During the process of SES shift, the rational allocation and use of water resources can shape an ideal regime that promotes regional ecosystem restoration. The empirical connections between the different phases of SES in the regime shift, their drivers, and their adverse or beneficial impacts provide valuable insights for sustainable SES management. Lessons from basin management that solely pursues single goals and focuses on local aspects, without considering these connections, have significant implications for long-term planning and policy formulation in arid basins worldwide.