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The hydrophilic flocculation of pyrite fines in aqueous suspensions with corn starch was studied by measuring particle size distribution, microscopy observation and micro-flotation. Furthermore, the interaction of corn starch with pyrite was investigated by determining the adsorption density and based on zeta potential measurements and X-ray photoelectron spectrometer (XPS) analysis in this work. The results of the particle size distribution measurement show that corn starch can effectively aggregate pyrite fines, and the pyrite floccules (flocs) are sensitive to mechanical stirring. The micro-flotation results suggest that the mechanical entrainment of pyrite fines in flotation can be effectively eliminated through the formation of large-size flocs. The zeta potential of pyrite particles decreases with the addition of corn starch. The XPS results prove that carboxyl groups are generated on the digested corn starch, and both iron hydroxyl compounds and ferrous disulfide on the pyrite surface can chemically interact with the corn starch digested by sodium hydroxide.