A method and a system for configuring an enhanced dedicated channel transmission bearer mode are provided by the present invention. The method comprises: in a situation that a first radio network controller (RNC) establishes an enhanced dedicated channel cell over a non-main carrier frequency layer in a predetermined network element, the first RNC configuring an enhanced dedicated channel transmission bearer mode of the predetermined network element, wherein the predetermined network element comprises at least one of the following: a node B connected to the first RNC and a second RNC connected to the first RNC. The present solution solves the problem in the related art that: the radio network controller cannot distinguish the received data from a main carrier and the received data from an auxiliary carrier.