To reveal the relationship between rural development and ecosystem services and to assist in efforts to balance these factors, we used a coupling model to carry out a study of the relationship between rural development and ecosystem services in Fujian Province of China during the years 2000 to 2015. First, we characterized the degree of rural development for each county in the province by calculating its index of relative rurality (IRR) and classified the counties into rural development types. Second, we calculated the values of three ecosystem services (ES) and overlapped them to get the sum of ES for each county. Third, we calculated the coupling and coupling coordination degree and analyzed the correlation between IRR and ES in the study area. The results showed that the mean value of IRR declined over the study period, was positively correlated with ES, and the correlation degree increased year by year. Meanwhile the degree of coupling was in the antagonistic stage, but tended to run in stage with a highly coordinated stage coupling coordination degree, if the business services type-counties were excluded. Although the overall coupling coordination degree was high, it declined yearly, which meant that rural development and ecosystem services increasingly lacked coordination. This paper supports and verifies some achievements of rural development programs in the research area, provides theoretical and decision-making support for coordinated rural development and ecosystem services protection in China, and provides a regional case study that could assist with similar research in other countries.