Sensitivity and data processing speed are important in spectral domain Optical Coherence Tomography (SD-OCT) system. To get a higher sensitivity, zero-padding interpolation together with linear interpolation is commonly used to re-sample the interference data in SD-OCT, which limits the data processing speed. Recently, a time-domain interpolation for SD-OCT was proposed. By eliminating the huge Fast Fourier Transform Algorithm (FFT) operations, the operation number of the time-domain interpolation is much less than that of the zero-padding interpolation. In this paper, a numerical simulation is performed to evaluate the computational complexity and the interpolation accuracy. More than six times acceleration is obtained. At the same time, the normalized mean square error (NMSE) results show that the time-domain interpolation method with cut-off length L = 21 and L = 31 can improve about 1.7 dB and 2.1 dB when the distance mismatch is 2.4mm than that of zero-padding interpolation method with padding times M = 4, respectively. Furthermore, this method can be applied the parallel arithmetic processing because only the data in the cut-off window is processed. By using Graphics Processing Unit (GPU) with compute unified device architecture (CUDA) program model, a frame (400 A-lines × 2048 pixels × 12 bits) data can be processed in 6 ms and the processing capability can be achieved 164,000 line/s for 1024-OCT and 71,000 line/s for 2048-OCT when the cut-off length is 21. Thus, a high-sensitivity and ultra-high data processing SD-OCT is realized.