The flexibility in frequency allocation is essential for high throughput satellites (HTS). The digital channelizer based transponder system has a crucial role in enhancing the performance of HTS. In this work, the design and implementation of a low computational complexity digital channelizer for HTS is proposed. The proposed reconfigurable filter structure for digital channelizer is to generate non-uniform and sharp transition width FIR filters for transponder of the satellite systems. The multipliers and group delay needed in the digital channelizer that employ the proposed structure are reduced when compared to FRM and traditional IFIR based digital channelizer. An example is used to illustrate the effectiveness of the proposed design. Results reveal that the proposed structure has a lower multiplier complexity than existing techniques. The proposed structure once implemented effectively, the power dissipation and hardware complexity are reduced. With the help of CSD, MOABC, and SIDC-CSE optimization, the filters used in this structure are made multiplier-less. Hence this structure is adaptable for the digital channelizer in the transponder of the satellite communication systems.