Disclosed is a method for operating a CDMA channel in a base transceiver station (BTS). The method for operating the CDMA channel in the BTS includes variably generating a CDMA channel list message transmitted from the BTS to a mobile station (MS) in a CDMA mobile communication system according to the BTS and a frequency allocation (FA) within the BTS, so as to variably operate the CDMA channel by the BTS and the FA. The method according to an embodiment of the present invention also includes variably allocating a CDMA frequency number group by the BTS and the FA in accordance with a CDMA channel index, a CDMA channel ID, and a CDMA channel kind, so that the CDMA channel is operated between BTSs and further by the FA, independently, thereby optimizing the CDMA frequency operation between the BTS and the MS.