Ecosystem service values (ESV) are strongly influenced by the vegetation cover, which is heterogeneous across different vegetation types. We develop a dynamic evaluation model of ESV for Wuyishan National Park Pilot adjusted by the rate of inflation and the fractional vegetation cover, which is calculated by an enhanced vegetation index from 2000 to 2018. The spatio-temporal variation of vegetation was also examined. The results demonstrated that: (1) the unit area of ecosystem service values adjusted by vegetation cover (ESV_VC) shows a gradient of forest > tea plantation > grassland > cropland, and the major ecosystem services provided by forests include soil formation and conservation, climate regulation, and biodiversity maintenance; (2) the ESV_VC increased to 2.1 billion yuan (The reference rate announced by the People’s Bank of China is the US dollar to 6.42 Yuan per dollar.) from 2000 to 2018. Higher and lower ESV_VC are predominant in the northwest and southeast region, respectively. In addition, changes of ecological protection structures and human disturbances negatively affected vegetation cover, leading to a decreased ESV_VC from 2000 to 2005 in the Jiuqu Stream Ecological Protection Area and the Wuyishan National Scenic Spot. The implementation of ecological protection policies from 2010 to 2018 enhanced the ESV_VC in the study area; and, (3) the ESV_VC is highest in the southeast and 25°–35° area with altitudes of 800–1000 m. Our model can provide timely and helpful information of changes in ESV for use in ecological corridor design and ecological security monitoring.