The invention discloses a method for processing a multilayer flexible circuit board, which comprises the following steps: punching a notch at two ends of a bended area of an inner layer circuit copper foil hot-pressed with an inner layer covering film respectively; reserving most of the bended area of an inner layer circuit in the subsequent process steps; and taking out reserved most of the bended area of the inner layer circuit until the last process step so that the hollow cut area of the inner layer circuit board copper foil in the subsequent process steps is reduced, the swelling and shrinking ratio of the inner layer circuit board copper foil in the subsequent process steps is reduced, and furthermore, the probability for each outer layer circuit on an outer layer circuit board copper foil to deviate from a corresponding drilling position of the inner layer circuit is reduced. Besides, in the subsequent process steps, the bended area of the outer layer circuit board copper foil compounded to the inner layer circuit board copper foil is not sunken to avoid steps appearing at the edge of the bended area of the outer layer circuit board copper foil so as to avoid the phenomenon of bad exposure and bubbles appearing in the covering film when the covering film is in hot pressing.