Satellite communication systems have attracted considerable attention recently because they can communicate in various conditions, including terrestrial, airspace, and marine terrain. In addition, high-throughput satellites (HTSs) that allow high-speed and large-capacity communication are currently being launched. However, the allocation of communication resources to each beam is fixed in conventional HTSs, which exhibit low flexibility under state changes. This includes requests to the satellite communication systems or environmental changes around the systems. Therefore, the use of a digital channelizer in a satellite communication system can allocate frequency resources to each beam. However, even if a digital channelizer is used, conventional frequency resource allocation methods that consider inter-beam interference do not use the same frequency resource as the adjacent beam. As a result, the frequency resources cannot be used effectively. To alleviate this issue, we propose a frequency resource allocation method with inter-beam interference so that the satellite communication system can allocate frequency resources more flexibly. In addition, we extend the conventional flexibility analysis model such that it quantifies the flexibility more accurately. Finally, the effectiveness of the proposed method is demonstrated under state changes of the satellite communication system using the extended flexibility analysis model.