In recent decades, conventional intensive agricultural practices have led to serious non-point-source pollution in China and have imposed serious ecological threats to agroecosystems, especially in ecologically sensitive areas. The Middle Line of the South-to-North Water Diversion project, which covers one of the largest ecologically sensitive areas in China, began in December 2014. In the study area around the Danjiangkou Reservoir belonging to the Middle Line of the South-to-North Water Diversion project, organic farming has been encouraged instead of conventional farming. This study aimed to measure the difference in ecological safety between conventional and organic farming based on the ecological footprint combined with life cycle assessment, which integrated the assessments of carbon footprint (CF), water footprint (WF) and nitrogen footprint (NF). This paper hypothesized that the ecological footprint of organic farming in the target area would be lower than that of conventional farming because of the reduced chemical inputs. The results showed that, as expected, first, organic farming had a lower footprint with a higher ecological remainder than conventional farming in 2015, indicating that organic farming practices made greater contributions to regional ecological safety in the study area. Second, in conventional farming, the total grey water footprint (nitrogen, phosphorus pentoxide and potassium oxide) was much higher than that of the farms in which only nitrogen fertilizer were used, indicating that both phosphorus pentoxide and potassium oxide also play indispensable roles in water footprint evaluation. Third, the energy-related nitrogen footprint was greatest in organic farming, caused by higher diesel oil consumption due to greater farm size for mechanical operation. Finally, the methods of calculating the amount of ecological compensation were improved. According to reduced ecological footprints, an extra payment (CF = 115.17 CNY ha−1; WF = 0.09 CNY ha−1; NF = 102.20 CNY ha−1) for organic farming should be seriously considered by different stakeholders, due to its benefit to greater ecological safety. From the perspective of ecological footprints, ecological compensation policies for organic farming might effectively promote ecological safety in the South-to-North Water Diversion watershed in the future. Footprint, as an accounting tool, offers great potential in assessment of ecological safety and ecological compensation worldwide and needs to be further explored in more dimensions such as phosphorus footprint, biodiversity footprint and so on.