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Excessive reclamation and improper use of agrochemicals in karst areas leads to serious non-point source pollution, which is of great concern and needs to be controlled, since contaminants can easily pollute groundwater due to the thin patchy soil and developed karst structures. The occurrences of organochlorine pesticides (OCPs) in karst soil were investigated by analyzing 25 OCPs in the karst soils near the Three Gorges Dam, China. The total concentrations of OCPs ranged 161–43,100 (6410 ± 9620) pg/g, with the most abundant compounds being p,p’-DDT and mirex. The concentration differences between the orchard and vegetable field and between upstream and downstream presented the influences of land-use type and water transport on the OCP spatial distributions. Composition analysis indicated the possible fresh inputs of lindane, technical DDT, aldrin, endrin, mirex, and methoxychlor. Their illegal uses implied an insufficient agrochemical management system in undeveloped karst areas. Principal component analysis with multiple linear regression analysis characterized the dominant sources from current agricultural use and current veterinary use in the study area. OCPs in the soils might not pose significant cancer risk for the residents, but they need to be controlled due to their illegal uses and bioaccumulation effect via the food chain.