In order to study the interface boundary structure, a three dimensional Near-Coincidence Site Lattice(3D-NCS) analysis based on Coincidence Site Lattice(CSL) theory has been proposed. In this method, coincidence atoms are calculated by a computer based, atomic matching procedure. To examine the validity of the 3-D NCS analysis, the comparison between this method with the O-lattice theory was made for the preferred orientation relationships in BCC/FCC system. A good correspondence is obtained. As for interface boundary structure, the 3D-NCS analysis is compared with the experimental results obtained by HRTEM observation of an (α+β) two phase titanium alloy. The NCS analysis is able to predict well the α/β interface boundary structure observed experimentally. Therefore, it is suggested that the 3D-NCS analysis is a useful method to predict the structure of interface boundary.