Rapidly and accurately extracting tobacco plant information can facilitate tobacco planting man-agement, precise fertilization and yield prediction. In karst plateau of southern China, tobacco plant identification is affected by large ground undulations, fragmented planting areas, complex and diverse habitats and uneven plant growth. This study took a tobacco planting area in Gui-zhou Province as the research object and used DJI UAVs to collect UAV visible light images. Considering plot fragmentation, plant size, presence of weeds and shadow masking, this area was classified into eight habitats. The datasets of different habitats were constructed to train the U-Net model. The results show that (1) the overall precision, recall, F1-score and IOU of tobacco plant information extraction were 0.68, 0.85, 0.75 and 0.60, respectively. (2) The precision was the highest for the subsurface-fragmented and weed-free habitat and the lowest for the smooth-tectonics and weed-infested habitat. (3) The weed-infested habitat with smaller tobacco plants can cause blurred images, reducing the plant identification accuracy. This study verified the feasibility of the U-Net model for tobacco single-plant identification in complex habitats. Decomposing complex habitats to establish the sample set method is a new attempt to improve crop identification in complex habitats in karst mountainous areas.