This report presents an advanced analysis of the optics of optical coherence tomography (OCT) systems. Study indicates that spectral filtering functions are contributed by the system optics, the coupling efficiency of both sample and reference arms, and the position of the sample relative to the optics. Simulations by advanced optical software, experiments on two existing OCT systems and the modified theoretical formula demonstrate that the different optics give different filtering functions. These filtering function narrow down the spectrum, shift the center of the spectrum and drop the amplitude of the intensity. Defining a composite standard deviation and a composite center wavelength of the two filtered spectra, we developed a new formula to describe the interference term of OCT, which clearly indicates the detail of the filtering function. An experiment in an extreme condition has been investigated in one of our existing OCT systems. We placed a narrow bandwidth filter into the reference arm. The filter has a center wavelength of 1313.6 nm with a full bandwidth of 6.4nm. The light source has a center wavelength of 1292nm with a bandwidth of 34nm. Experimental resolutions are 19 microns and 85 microns, with and without filter respectively. The calculations are 21.6 and 85.5 microns, respectively, using our new formula.