The National Key Ecological Functional Areas (NKEFAs) of China rely on the main functional area planning, with the core goal of enhancing the supply of ecological products. Carbon sink is an important ecological product, and it is necessary to understand whether the establishment of NKEFAs has enhanced vegetation carbon sink (CS). Considering the establishment of NKEFAs as a quasi-natural experiment, based on the panel data of prefecture-level cities in China from 2001 to 2019, a time-varying difference-in-differences (DID) model is used to systematically examine the impact of NKEFAs on CS. The study found that the establishment of NKEFAs has significantly enhanced the CS, and compared to the non-NKEFAs, NKEFAs has increased CS in the covered areas by an average treatment effect (ATE) of 2.1625. The establishment of NKEFAs can enhance CS through the optimization of territory spatial structure, the upgrading of industrial structure and the inter-industrial mobility of labor. The enhancement roles of NKEFAs on CS are heterogeneous across different functional area types, geospatial locations, and quantile levels, with higher enhancement of CS at windbreak-sand fixation type, northwestern region and high quantiles, respectively. In addition, NKEFAs not only have a significant positive ecological spillover effect, but also balanced with local economic growth, they achieve the goals of "lucid waters and lush mountains are invaluable assets".