The invention belongs to the technical field of purification of polysilicon by a physical metallurgical technology. A method for purifying the polysilicon by adopting an electron beam to carry out fractionated smelting comprises the following steps: firstly preparing a material; placing a cleaned and dried silicon material into an electronic beam smelting furnace; carrying out preprocessing; carrying out water cooling on a crucible and preheating an electronic gun; and finally purifying, i.e. melting and smelting for a certain time by adopting the electron beam with a small beam current of 200 to 300mA, then reducing the beam current to zero, smelting the polysilicon for a certain time by the small beam current of 200 to 300mA and stopping the beam current after a silicon ingot is completely darkened and silicon steam is condensed back into a molten pool, repeatedly repeating the operation of smelting small beam current and stopping beam current, and finally carrying out cooling and condensing to obtain a polysilicon ingot with low phosphorus content. The method has the obvious effects that due to the adoption of the technology of carrying out electro beam fractionated smelting, the evaporation loss of silicon is reduced; the method has good purifying effect, stable technology, simple process, short period and high production efficiency; energy is saved; and consumption is reduced.