Phase fluctuations in a two-transverse-dimensional scanning Fourier domain optical coherence tomography (FDOCT) seriously affect in vivo phase related applications. The phase difference between two A-scans sampled at the same scanning position or adjacent scanning position is acquired by matching of the phase distribution characteristics on the surface of two A-scans. Finger and palm scanning experiments are performed and defocused images of finger and palm are recovered based on Fresnel scalar diffraction algorithm by using phase compensated OCT complex signals. To further prove the performance of the proposed method, human eye scanning experiments are also performed and blood flow images of retina are extracted from the phase registration results. The accurate, fast and simple phase compensation method is critical for in vivo phase related applications.