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The South China Karst, a United Nations Educational, Scientific and Cultural Organization (UNESCO) natural heritage site, is one of the world’s most spectacular examples of humid tropical to subtropical karst landscapes. The Libo cone karst in the southern Guizhou Province is considered as the world reference site for these types of karst, forming a distinctive and beautiful landscape. Geomorphic information and spatial distribution of cone karst is essential for conservation and management for Libo heritage site. In this study, a deep learning (DL) method based on DeepLab V3+ network was proposed to document the cone karst landscape in Libo by multi-source data, including optical remote sensing images and digital elevation model (DEM) data. The training samples were generated by using Landsat remote sensing images and their combination with satellite derived DEM data. Each group of training dataset contains 898 samples. The input module of DeepLab V3+ network was improved to accept four-channel input data, i.e., combination of Landsat RGB images and DEM data. Our results suggest that the mean intersection over union (MIoU) using the four-channel data as training samples by a new DL-based pixel-level image segmentation approach is the highest, which can reach 95.5%. The proposed method can accomplish automatic extraction of cone karst landscape by self-learning of deep neural network, and therefore it can also provide a powerful and automatic tool for documenting other type of geological landscapes worldwide. Full article