In order to clarify the destruction mechanism of large structures in large seismic movements, a non-contacting displacement measurement system with a three-dimensional dynamic position with high precision is required. We have developed a three-dimensional measuring system with image processing using optical motion capture technology. This system consists of light emitting markers installed on the object structure and plural high speed cameras which obtain images of markers’ movement simultaneously, to measure the dynamic position of the three dimensional spatial coordinates of the markers. In order to measure the dynamic position with high precision, we have ever developed sub-pixel processing method which is able to measure very small displacements of the markers by analyzing the luminance distribution. Moreover, we have developed a new marker of spherical surface emission type which formed the luminance profile to improve furthermore the accuracy in rotational movement. Shaking tests were carried out with this measuring system and the results indicated that this system using new markers had sufficient accuracy within errors of a few millimeters in the structure of a 4 meter cube. Consequently, we have acquired the potential to apply to the measurement to the 3-D Full Scale Earthquake Testing Facility (E-Defense).