The pyrite in the nature, due to the differences of the semiconductor properties caused by crystal structure and the presence of defects, will be bound to seriously affect the surface state and surface-activity of the mineral, eventually make the process of electrochemical reaction and flotation behavior change in the solution. Starting from the microscopic point of view, this article would study the affect mechanism of crystal structure and defects on the pyrite surface properties and the electrochemical reaction process. Studies have shown, because of the existence of the strong Fe-S covalent bond and determinate equilibrium defects, make the Fermi level and valence state of partial surface element change, accordingly lead to special semiconductor and surface properties of pyrite, ultimately affect the process of pyrite electrochemical flotation.