Over nearly seven decades, China’s comprehensive system of nature reserves has been meticulously constructed, encompassing national, provincial, city, and county-level reserves that span diverse ecosystems and species. However, despite garnering considerable attention, there remains a noticeable research gap concerning the spatiotemporal variations in vegetation ecological quality and its driving forces within national-level nature reserves. The study analyzed changes in the Vegetation Ecological Quality Indicator (VEQI) within China’s national nature reserves from 2002 to 2022, encompassing natural factors, human activities, and future trends prediction. Additionally, it evaluated the impacts of ecological restoration and climate change on VEQI. The study revealed that the average VEQI value in China’s national nature reserves was 3.741 from 2002 to 2022, indicating a notable increase of 17.63%. A significant portion, encompassing 48.63×104 km², demonstrated an upward VEQI trend, whereas 29.36×104 km² exhibited a declining trend, emphasizing the overall upward trajectory of VEQI in China’s nature reserves. Approximately 3.2% of the total area was affected by the combined inhibitory impacts of human activities and climate change, with an additional 17.5% affected solely by climate change factors. Overall, the VEQI of China’s nature reserves exhibited an upward trend, with natural factors and human activities playing pivotal roles in driving these changes. Looking ahead, there is evident spatial heterogeneity in the VEQI trend within China’s national nature reserves, with approximately 64.3% of the areas experiencing an increase. This research endeavor contributes to the existing literature by furnishing scientific data to underpin assessments of vegetation ecological quality within China’s national nature reserves. It adds to the body of knowledge and may inform the formulation of environmental protection policies.