A system and method for dynamically allocating channels in a wireless communication system including multiple sub-channels and multiple frame cells, each of the sub-channels being an assembly including a preset number of sub-frequency bands divided from an overall frequency band, the frame cells using each of the sub-channels as a basic transmission unit and having a frequency domain and a time domain occupied by the sub-channels. A mobile station transmits channel quality information of frame cells to an access point. An access router transmits channel allocation information about the multiple frame cells and sub-channels determined according to the received channel quality information to the access point, and the access point receives the channel allocation information about the multiple frame cells and sub-channels, compares the channel allocation information with newest channel quality information, and allocates a sub-channel of a frame cell selected according to the comparison to the mobile station.