A method and apparatus for pulse electrochemical polishing a wafer are disclosed. The method comprises steps of: establishing a duty cycle table showing all points on the wafer, a removal thickness corresponding to every point and a duty cycle corresponding to the removal thickness; driving a wafer chuck holding and positioning the wafer to move at a preset speed so that a special point on the wafer is right above a nozzle ejecting charged electrolyte onto the wafer; looking up the duty cycle table and obtaining the removal thickness and the duty cycle corresponding to the special point; and applying a preset pulse power source to the wafer and the nozzle and the actual polishing power source for polishing the special point being equal to the duty cycle multiplying by the preset power source.