<p>Territorial spatial ecological restoration is a crucial prerequisite for optimizing the territorial spatial patterns, enhancing the ecosystem functions, and achieving sustainable development at the regional scale. The Qaidam Basin, located in the alpine arid region of the Qinghai–Xizang Plateau, China, is experiencing desertification, biodiversity loss, soil erosion, and environmental pollution. Selecting the Qaidam Basin as the study area, we identified 9 ecological sources in the region using the Morphological Spatial Pattern Analysis (MSPA) method and the landscape connectivity assessment, and extracted 10 significant corridors and 26 general corridors using the Minimum Cumulative Resistance (MCR) and Gravity models. Then, we determined 114 ecological “pinch points” and 42 ecological barrier points by employing the Circuit Theory, thereby constructing the ecological security pattern of the area. Further, we evaluated the ecosystem health of the Qaidam Basin during 2003–2023 using the Vitality–Organization–Resilience–Service (VORS) model. Finally, we integrated ecosystem health assessment and ecological security pattern to comprehensively identify the key areas for ecological restoration in the Qaidam Basin. The results revealed that the ecosystem in the basin fluctuated toward a healthier state from 2003 to 2023. The average ecosystem health index (EHI) for the basin decreased from 0.34 in 2003 to 0.28 in 2013, followed by a substantial recovery to 0.36 in 2023. Higher EHI values were found in the northeastern, southeastern, and southwestern fringes and lower values were located in the basin interior and northwestern region. During 2003–2023, the areas that exhibited a decrease in EHI were primarily located in the interior and northwestern regions of the basin, while those that exhibited an increase in EHI were located in the northeastern, southeastern, and southwestern fringes, demonstrating expanded spatial differences. This may be attributed to the fact that once an eco-environment is damaged, the ecological recovery of the vulnerable areas within the eco-environment will be slow and difficult. This study identified four types of ecological restoration areas, including corridor connectivity, artificial restoration, ecological recovery, and ecological enhancement zones, covering a total area of 6034.7 km², and proposed targeted ecological restoration strategies according to these different categories. Our findings can serve as a valuable reference for optimizing the territorial spatial patterns, enhancing the ecosystem functions, and promoting sustainable development in the Qaidam Basin.</p>