The nonuniform distribution of interference spectrum in wavenumber k-space is a key issue to limit the imaging quality of Fourier-domain optical coherence tomography (FD-OCT). At present, the reconstruction quality at different depths among a variety of processing methods in k-space is still uncertain. Using simulated and experimental interference spectra at different depths, the effects of common six processing methods including uniform resampling (linear interpolation (LI), cubic spline interpolation (CSI), time-domain interpolation (TDI), and K-B window convolution) and nonuniform sampling direct-reconstruction (Lomb periodogram (LP) and nonuniform discrete Fourier transform (NDFT)) on the reconstruction quality of FD-OCT were quantitatively analyzed and compared in this work. The results obtained by using simulated and experimental data were coincident. From the experimental results, the averaged peak intensity, axial resolution, and signal-to-noise ratio (SNR) of NDFT at depth from 0.5 to 3.0$$mm were improved by about 1.9$$dB, 1.4 times, and 11.8$$dB, respectively, compared to the averaged indices of all the uniform resampling methods at all depths. Similarly, the improvements of the above three indices of LP were 2.0$$dB, 1.4 times, and 11.7$$dB, respectively. The analysis method and the results obtained in this work are helpful to select an appropriate processing method in k-space, so as to improve the imaging quality of FD-OCT.