Invasive species face new selective pressures and low genetic variation caused by genetic bottlenecks and founder effects when they are introduced into novel environments. Epigenetic variation may help them to cope with these problems. Mile-a-minute (Mikania micrantha Kunth) is a highly invasive exotic weed that has seriously damaged biodiversity and agricultural ecosystems. We first adopted methylation-sensitive amplified polymorphism (MSAP) markers to investigate epigenetic variation of 21 M. micrantha populations in southern China, and further explored the effects of environmental factors on population epigenetic differentiation by correlating epigenetic and climate and soil data. Adaptive epiloci positively correlated with climate/soil variables were identified. Minimum temperature of the coldest month and mean temperature of the coldest quarter were considered as decisive factors for its distribution. Climate is presumed to play a relatively more important role than soil in shaping the adaptive epigenetic differentiation in M. micrantha. Under ongoing global warming, populations of M. micrantha are predicted to expand northward. In addition, the weed also presented higher epigenetic variation compared with genetic variation. Leaf shape variation was detected related to methylation-state change at the population level.