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Rapid dewatering and thickening of whole-tailings with ultrafine particles is one of the most important processes for the whole-tailings paste preparation. Deep-cone thickener, a kind of such process for the flocculation and settling of whole-tailings, is particularly necessary to study. However, there exist many problems in observing the flocculation and settling process of whole-tailings, as well as the particle size distribution (PSD) of whole-tailings floccules in deep-cone thickener. Population balance model (PBM) is applied to predict the PSD in deep-cone thickener, and LUO model and GHADIRI model are employed to study the aggregation and fragmentation mechanism of the whole-tailings particles, respectively. Through three-dimensional numerical simulation on the whole-tailings flocculation and settling in deep-cone thickener using computational fluid dynamics (CFD)-PBM, the distribution of density and turbulent kinetic energy in deep-cone thickener were obtained, at the same time the spatio-temporal changes of whole-tailings floccules particle size distribution are analyzed. Finally, the major flocculation position in deep-cone thickener is found and the flocculation settling rules of whole-tailings are achieved.