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It is necessary to devise the efficient FFT algorithm which can reduce computational complexity due to multiplication in the butterfly structure with twiddle factors in the OFDM based Cognitive Radio, where zero valued inputs/outputs outnumber nonzero inputs/outputs. Now transformed decomposition is considered as more suitable candidate than FFT pruning method for OFDM based Cognitive Radio due to the feasibility of HW design about irregular position of zero inputs/outputs. However, with the introduction of the efficient control circuit for the pruning matrix which selects the multiplication branch corresponding to nonzero outputs in OFDM based cognitive radio, the split-radix FFT pruning algorithm can be proposed for getting the more reduction of computational complexity. Through analyzing and comparing the computation complexity about the split-radix FFT pruning algorithm with other algorithms, it was shown that the proposed method is more efficient than other conventional algorithms for the reduction computational complexity.