A method and a system for intra-BS carrier handover are provided. The method comprises: a mobile station scanning predetermined carriers within the base station based on predetermined rules; obtaining a scanning report comprising channel quality information of part of or all of the predetermined carriers; and sending the scanning report to the base station; the base station obtaining the channel quality information in the scanning report; selecting a target carrier from the predetermined carriers; and informing the mobile station of the selected target carrier via a message; and the mobile station handing over to the target carrier in a predetermined manner in response to the message. By using the method, seamless handover of intra-BS carriers can be performed in a multi-carrier system for ensuring the service continuity of the mobile station to eliminate carrier handover time delay.