The study of farmland carbon footprint is of great significance to farmland ecosystem management and sustainable agricultural development. It can also characterize the ecological effects of farmland expansion. Based on the county-scale statistical data and spatial analysis, we studied the temporal and spatial changes of the carbon footprint of the Yunnan farmland ecosystem over the past 30 years. The results showed that:during the period from 1985 to 2015, the average annual increase of carbon emissions from farmland ecosystems in Yunnan Province was 13.9%. The contribution of carbon emissions from chemical fertilizer was the largest, accounting for 56%. In 2015, the carbon emissions per unit area reached 331.6 kg/hm². The average annual increase rate of carbon absorption of farmland ecosystems in Yunnan Province was 3.04%. Rice had the largest proportion of carbon absorption, accounting for 41% of the total carbon absorption, whereas corn had the fastest growth rate of carbon absorption at 8.76%. There was a carbon surplus in farmland ecosystems in Yunnan Province. Furthermore, the overall carbon footprint showed a growing trend with the average annual growth rate of 16.8%, and the carbon footprint per unit area increased continuously. From the spatial point of view, the carbon emission and carbon absorption of farmland ecosystems in Yunnan Province had similar spatial distributions, which appeared more in the southeast and less in the northwest. However, the carbon footprint was spatially distributed more in the east and west and less in the middle. Their most obvious features were large regional differences and variation range.