The monetary value assigned to ecosystems and their essential goods and services is known as ecosystem service value (ESV). Fragile ecological environments, susceptible to climate change and human disturbances, require significant ecological protection. This protection is vital not only for stabilizing socio-economic conditions but also for fostering a positive feedback loop within natural systems. Looking ahead, identifying priority conservation areas and regions of particular concern in fragile environments based on ESV changes is a proactive approach. Until now, current studies on ESV in fragile ecological environments have been insufficient, falling short of adequately serving the purpose of ecological protection in such areas. The Hexi region (HXR), situated in the interlaced area of the Qilian Mountains and the Alxa Plateau in northwest China, possesses a fragile ecological environment. Due to the intricate interactions between humans and the environment, it stands out as a crucial area for studying ecosystem services in fragile habitats. Hence, this study aims to systematically analyze the ESV in the HXR over the past 30 years. Here, the values of 11 ecosystem service categories in HXR during 1990–2020 were calculated, clarifying their spatiotemporal difference and dynamic changes based on land use/cover (LULC) products for years 1990, 1995, 2000, 2005, 2010, 2015, and 2020, using an improved equivalent factors method. The findings revealed that the unit standard equivalent factor is 1.51 × 105 CNY·km−2·a−1, and the total ESV value has grown from CNY 182.50 to 185.48 billion from 1990 to 2020. Hydrologic regulation, climate regulation, and soil conservation service values are the principal single ESV categories across HXR. Over the past three decades, ESV changes in HXR have been primarily driven by water area, grassland, and wetland, with the sensitivity of ESV to LULC generally increasing (0.15~9.10%). Natural forcing and anthropogenic perturbations have combined to cause changes in LULC in HXR, influencing ESV fluctuations. Future ecosystem protection activities in HXR should prioritize the maintenance of grasslands, water regions, and wetlands to ensure the preservation of ESV. This study clarifies the impacts of LULC change on ESV in fragile natural environments and highlights the significance of focusing on ESV changes for the health promotion of natural-social systems. The findings provide a foundation for constructing a sustainable development model that is in harmony with both people and the environment.