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State-of-art quantum key distribution (QKD) systems are performed with several GHz pulse rates, meanwhile privacy amplification (PA) with large scale inputs has to be performed to generate the final secure keys with quantified security. In this paper, we propose a fast Fourier transform (FFT) enhanced high-speed and large-scale (HiLS) PA scheme on commercial CPU platform without increasing dedicated computational devices. The long input weak secure key is divided into many blocks and the random seed for constructing Toeplitz matrix is shuffled to multiple sub-sequences respectively, then PA procedures are parallel implemented for all sub-key blocks with correlated sub-sequences, afterwards, the outcomes are merged as the final secure key. When the input scale is 128 Mb, our proposed HiLS PA scheme reaches 71.16 Mbps, 54.08 Mbps and 39.15 Mbps with the compression ratio equals to 0.125, 0.25 …