The concept of Internet of Things (IoT) has attracted much research attention for the realization of a smart society. However, the radio transmission coverage of the existing IoT solutions is not enough to connect lots of devices deployed over wide areas. Therefore, satellite networks have been considered as one of the most attractive solutions to wide cell coverage of IoT, i.e., global-scaled IoT. In satellite communication, a digital channelizer is one of the most significant parts that support multiple transponders. Owing to their wide coverage, satellite communication systems are more vulnerable to interference than other types of wireless communication systems. In this study, a cognitive interference cancellation using the inherent properties of a digital channelizer is considered. The proposed method detects a subchannel corrupted by interference and omits it. A simple energy detection method and a modified version are proposed for detection of interference. In the modified (i.e., improved) method, the number of required signal blocks to achieve the target detection performance can be reduced, i.e., the detection performance is improved with the same number of blocks, by exploiting the property of the fast Fourier transform (FFT) algorithm. Detection performance such as false alarm and detection probabilities are analyzed, and the validity of the analysis is verified with numerical results. It is also shown that an interference lower than a certain level in the proposed approach does not need to be cancelled.