A wireless communication system and a channel changing method thereof are provided. The wireless communication system which includes a plurality of channels, uses one of the plurality of channels as a specific channel, and uses another channel of the plurality of channels as a communication channel, includes: a base terminal for obtaining the one of the plurality of channels as an alternative channel, generating a channel change command including information on the alternative channel, and transmitting the command on a specific channel, when there is a data error received on the communication channel; and a wireless input device for resetting the alternative channel as a new communication channel and performing wireless communication on the communication channel which was reset, after obtaining the information on the alternative channel by receiving the channel change command from the specific channel. Accordingly, the base terminal can obtain the alternative channel by quickly sensing the channel cross talk so that a channel change can be performed immediately and actively, thereby enhancing the reliability and efficiency of the wireless communication.