According to deficiencies in design and practice of transfer payment to national key ecological function areas, 140 typical counties which received transfer payment to national key ecological function areas were selected in Gansu, Guizhou, Heilongjiang, Hebei, Anhui and Hainan provinces. The interregional synergy and the coupling coordination degree were analyzed for transfer payment to national key ecological function areas and eco-environmental protection expenditure in typical counties of different provinces and different ecological function areas. The results showed that there was significant difference (P<0.05) in the eco-environmental protection expenditure, pollution control expenditure, and the ecological restoration expenditure of typical counties in different provinces or different ecological function areas. The difference between transfer payment of typical counties in different provinces or different ecological function areas was not significant (P>0.05). In terms of the regional difference and type difference, there was no synergy between transfer payment to key ecological function areas and eco-environmental protection expenditure of typical counties. The coupling coordination degree between transfer payment and the eco-environmental protection expenditure, pollution control expenditure, and the ecological restoration expenditure in typical counties, provinces and ecological function areas was less than 0.4. The coupling coordination status between transfer payment and the eco-environmental protection expenditure was imbalance in the typical counties, provinces and ecological function areas in 2017. At present, the regional difference and type difference of eco-environmental protection expenditure was not be reflected for the fund allocation of transfer payment to national key ecological function areas, The synergy with eco-environmental protection expenditure was not reflected too. Further research is needed to innovate and improve fund allocation of transfer payment to national key ecological function areas.