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We have designed the spectral domain optical coherence tomography system using a broadband superluminescent diode laser source and home-built spectrometer, which acquires 2D or 3D images with high speed and high resolution. We have also introduced the N-point complex FFT algorithm, which is faster than 2N point real FFT, into the signal processing part, thus shortening signal processing time after image data acquisition. For the sake of convenient measurements, the spectral domain optical coherence tomography was manufactured in the form of a microscope. The volumetric image of a mouse anterior eye could be reconstructed from a few hundred 2D images.