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The National Key Ecological Function Zones (NKEFZ) serve as crucial ecological security barriers in China, playing a vital role in enhancing ecosystem services. This study employed the theoretical framework of ecological benefits assessment in major ecological engineering projects. The primary focus was on the ecosystem macrostructure, ecosystem quality, and key ecosystem services, enabling quantitative analysis of the spatiotemporal changes in the ecosystem status of the NKEFZ from 2000 to 2019. To achieve this, remote sensing data, meteorological data, and model simulations were employed to investigate five indicators, including land use types, vegetation coverage, net primary productivity of vegetation, soil conservation services, water conservation services, and windbreak and sand fixation services. The analysis incorporated the Theil–Sen Median method to construct an evaluation system for assessing the restoration status of ecosystems, effectively integrating ecosystem quality and ecosystem services indicators. The research findings indicated that land use changes in NKEFZ were primarily characterized by the expansion of unused land and the in of grassland. The overall ecosystem quality of these zones improved, showing a stable and increasing trend. However, there were disparities in the changes related to ecosystem services. Water conservation services exhibited a decreasing trend, while soil conservation and windbreak and sand fixation services showed a steady improvement. The ecosystem of the NKEFZ, in general, displayed a stable and recovering trend. However, significant spatial heterogeneity existed, particularly in the southern region of the Qinghai–Tibet Plateau and at the border areas between western Sichuan and northern Yunnan, where some areas still experienced deteriorating ecosystem conditions. Compared to other functional zones, the trend in the ecosystem of the NKEFZ might not have been the most favorable. Nonetheless, this could be attributed to the fact that most of these areas were situated in environmentally fragile regions, and conservation measures may not have been as effective as in other functional zones. These findings highlighted the considerable challenges ahead in the construction and preservation of the NKEFZ. In future development, the NKEFZ should leverage their unique natural resources to explore distinctive ecological advantages and promote the development of eco-friendly economic industries, such as ecological industry, ecological agriculture, and eco-tourism, transitioning from being reliant on external support to self-sustainability. [ABSTRACT FROM AUTHOR]