Selenium is one of the 15 essential trace elements necessary for the growth of animals, plants, and humans. It has the functions of scavenging free radicals, anti-oxidation and enhancing immunity, etc., but its safe dosage range is very narrow. The pyrite’s morphology prepared by wet ball milling was characterized by scanning electron microscope (SEM) and X-ray diffraction (XRD). SEM observations were found that the pyrite after the addition of ethanol was a spherical particle agglomerate with a relatively uniform particle size, ranging from 17 to 200 nm, with an average particle size of 138 nm. The characteristic peaks in the XRD diffraction pattern are the same as the positions of the peaks in the FeS2 diffraction pattern. Therefore, it is determined that the main chemical component in pyrite is FeS2, and there are no impurity peaks in the pattern, indicating that no impurities were mixed in the process of preparation. The sample purity is high. The experimental results show that this method’s pyrite has the advantages of small particle size, large specific surface area, and high reaction activity. In the research, X-ray photoelectron spectroscopy (XPS) was used to study the mechanism of removing Se(IV) by pyrite. The research results show that (1) In a relatively wide experimental pH range (pH 2.2~11.5), pyrite can effectively remove SeO2-3 and the removal efficiency (except pH 7.8) is above 90%; (2) After the reaction of pyrite with SeO2-3, the characteristic peaks of its main constituent elements appeared the left shift indicated that a certain chemical change had taken place on the surface of the pyrite; (3) The mechanism of removal of SeO2-3 with pyrite in an acid-base environment is a little different. In an acidic environment, the removal of SeO2-3 by pyrite is a simple redox process.That is, S2-2 activated by the acid in pyrite reduces Se(IV) to Se(0), and the stronger the acidity, the better the removal effect of SeO2-3; in the alkaline environment, the oxidation-reduction and complexation reactions coexist during the removal of SeO2-3, and the surface of pyrite has complexed Fe(OH)SeO3 and elemental Se(0) exist in two forms, and the stronger the basicity, the more the content of complexed Fe(OH)SeO3. The above research results provide an important theoretical basis and application basis for removing variable valence metal anions represented by SeO2-3 from water and soil by pyrite.