Radio resource allocation apparatus and method in a multi-channel system are provided. The method includes determining a type of a channel to be allocated to terminals, which request a resource allocation. When there is a terminal to be assigned the band AMC channel, necessary resources are allocated to the terminal as resources of the band AMC channel within a frequency band preferred by the terminal. A virtual resource space is generated which collects resources not allocated as the resources of the band AMC channel. Resources are allocated to terminals to be assigned the diversity channel from within the virtual resource space. Accordingly, the radio resources can be efficiently allocated in the multi-channel system where the diversity channel and the band AMC channel coexist.