The coupling coordination relationship between cultivated land and water resources in arid regions is crucial for ecological security and sustainable food production. This study explores the interaction between these resources to optimize the allocation of water–land resources, ecological resources, and agricultural resources and promote synergistic development. Taking the Turpan–Hami Basin as a case study, this research analyzed the utilization efficiency of cultivated land and agricultural water resources from 2000 to 2023 using a super-efficiency SBM-DEA model. A coupling coordination degree model was constructed to evaluate their coordinated development level, with spatial autocorrelation and other methods used to examine spatiotemporal patterns. Key findings include: (1) The overall utilization efficiency of both resources was relatively low, with mean values of 0.516 and 0.596, showing a fluctuating upward trend and significant spatial heterogeneity; (2) The mean coupling coordination degree (CCD) ranked as follows: Barkol Kazakh Autonomous County (0.587) > Yiwu County (0.563) > Gaochang District (0.494) > Shanshan County (0.437) > Tuokexun County (0.417) > Yizhou District (0.342), with an annual growth rate of 4.6%; (3) Regional disparities were dominated by intra-regional differences (42.0%), followed by transvariation density (30.64%). This study provides scientific evidence for optimizing resource allocation in arid regions.