The construction of green isolation areas is an important means to prevent the sprawl of central urban areas, guide the rational layout of urban green spaces, and protect the ecological environment. However, with the continuous construction advancement of green isolation areas in Beijing, the problems of mutual restriction between ecology and economy are increasingly prominent, but few studies are devoted to such problems. Taking the second green isolation area of Beijing in 2000, 2010, and 2020 as the research objects, the kilometer grids were taken as the basic research units, and the land cover data and GDP data were placed in the unified spatial coordinate system by GIS software; also, the equivalent factor method was adopted to calculate the ecological service value (ESV) of the research region, and the eco-economic harmony degree (EEH) was calculated using the ratio of ESPpr to GDPpr. This research innovatively used the kilometer grid as the basic research unit to study the second green isolation area in Beijing and compared the harmony degree between the second green isolation area and the overall ecological, economic system of Beijing, so as to dynamically compare the ecological environment changes in the second green isolation area during the study period and the degree of mutual influence in the process of economic development. The study found that the construction of the second green isolation area improved the harmony of the eco-economic system in a certain area, but it failed to effectively curb the spread of construction land in the urban area of Beijing. The research results can provide scientific guidance for the coordinated planning of the ecological economy in the second green isolation area.