A high-speed high-sensitivity swept source optical coherence tomography (SSOCT) system using a high speed swept laser source is developed. Non-uniform discrete fourier transform (NDFT) method is introduced in the SSOCT system for data processing. Frequency calibration method based on a Mach-Zender interferometer (MZI) and conventional data interpolation method is also adopted in the system for comparison. Optical coherence tomography (OCT) images from SSOCT based on the NDFT method, the MZI method, and the interpolation method are illustrated. The axial resolution of the SSOCT based on the NDFT method is comparable to that of the SSOCT system using MZI calibration method and conventional data interpolation method. The SSOCT system based on the NDFT method can achieve higher signal intensity than that of the system based on the MZI calibration method and conventional data interpolation method because of the better utilization of the power of source.