The self-developed high-speed three-dimensional swept optical coherence tomography (SS-OCT) system is reported. Based on fast swept laser technology, the system can realize high speed axial scan (A-scan) rate of 50 KHz. In order to shorten the development cycle, the system software is based on LabVIEW combining with Matlab. Which achieves modular design including timing control, data acquisition, data processing and image reconstruction. The system has a friendly interface and is easy to maintain. It utilizes an external clock uniform in K-space as triggers synchronously generated by the swept source—a K-trigger mode for data acquisition so that a uniform data sampling in K-space is enabled without any other linear wavenumber re-calibracation. Actually measured axial resolution of the system is 8.9 μm. The systerm sensitivity is experimentally determined to be above 100 dB in the whole depth range. This SS-OCT systerm is capable of realtime display of two-dimensional OCT and can obtain three-dimensional OCT with a measurement time of 1.8 s. Vivo human finger segments and apple peel tissue are investigated two- and three-dimensionally. The three-dimensional OCT volumes chearly show the structures of the fingerprint which are difficult to be observed in two-dimensional OCT images.