A method and apparatus of transmitting an uplink control signal of a mobile station (MS) in a wireless communication system is provided. A mobile station (MS) receives resource allocation information of a first uplink control channel for transmitting an uplink synchronization signal and resource allocation information of a second uplink control channel. The MS allocates a first uplink control channel resource and a second uplink control channel resource to the first uplink control channel and the second uplink control channel respectively based on the resource allocation information of the first uplink control channel and the resource allocation information on the second uplink control channel and transmits an uplink control signal through at least one of the first uplink control channel and the second uplink control channel to a base station. The first uplink control channel resource is located in a first resource unit among a plurality of resource units constituting a logical resource region, and the first uplink control channel resource and the second uplink control channel resource are allocated in that order in the logical resource region.