The invention discloses a system and a method for data storage of an FFT processor. The data storage system comprises a controller, a storage, a papilionaceous operation unit and a twiddle factor form; the storage is used for storing data; the twiddle factor form stores a twiddle factor needed for each papilionaceous operation according to the sequence; the papilionaceous operation unit is used for the papilionaceous operation; the controller comprises a papilionaceous operation counter, a series counter, an index number generator, an address mapping device, a delay unit and a twiddle factor serial number generator; the data storage method comprises the following steps that: according to the input sequence, input data is recorded as dindex, wherein, the index is equal to 0, 1, ..., N-1; the index is represented by a binary digit and needs m bits, wherein, the m is equal to log 2N, that is, recorded as index[m-1:0]; and the input data is stored in the storage. The system and the method for data storage of the FFT processor use a single-port storage to realize the conflict-free read-write access; and the utilization rate of the papilionaceous operation unit is nearly 100 percent, thereby effectively improving the utilization efficiency of hardware resource.