In 2009, the Ministry of Finance of the People's Republic of China issued the "National Key Ecological Function Area Financial Transfer Payment (Pilot) Method". Thereafter, the government began to make ecological compensation for the key national ecological function area with transfer payment. By 2020, the government had allocated 603.55 billion yuan for transfer payment. It is great significance to evaluate the ecology protection effect of financial transfer payment in the national key ecological function area. The previous studies on ecological system pattern have been carried out almost at national scale or regional scale. But the research on ecosystem pattern change in the national key functional areas since the transfer payment is lack. Therefore, this paper took the counties that got transfer payment in the national key ecological function area in 2019 as the evaluation objects. Multiple phases of the remote sensing of land use/land cover data were used to evaluate the performance of the financial transfer payment policy on ecosystem pattern and change in the national key ecological function area. Two evaluation aspects were ecosystem composition and its change, and ecosystem structure change and type conversion. Six evaluation indexes were area of ecosystem, composition of ecosystem, area change rate of ecosystem types, change direction of ecosystem types, comprehensive dynamic attitude of ecosystem, and land cover conversion index. The results showed that the ecological quality of the national key ecological functional area improved overall, and the land cover conversion index was 3.85% from 2011 to 2019. The improvement of ecological quality was mainly related to the increase of water area. After received the fund of national financial transfer payment, the ecological quality of all selected counties improved significantly. In 2011-2016, the method of spatial horizontal comparison was adopted. The results showed that the land cover conversion index of the counties that received the fund of financial transfer payment was 2.28%, while that of the other counties was-3.36%. In addition, the method of longitudinal comparison was adopted in 2011-2019. The results showed that the land cover conversion index was-3.35% before the counties received the fund of financial transfer payment, and increased to 1.70% after they received the fund of financial transfer payment. However, the interference of human activities in the national key ecological function area is still quite strong. During 2011-2019, the land area for urban and rural, industry, mining and residents increased by 14.2%, while the ecological space area such as forest and grass decreased. The ecological protection target of the national key ecological function area has not been effectively implemented. Therefore, the effective implementation of various national regulations on land space management, the effective resolution of the contradiction between ecological protection and economic development, and the scientific decision-making on ecological protection and restoration are urgent problems for the ecological protection in key functional area and counties.