X-ray focus projection coordinates are the important geometrical parameters for three-dimensional (3D) CT reconstruction. But for practical 3D-CT scanning system, it is impossible to measure the position of the X-ray focus projection by direct means. An improved method to measure the X-ray focus projection coordinates with high accuracy is proposed. Through acquiring digital radiographic (DR) images of the single ball object at different positions in the cone X-ray beam, the DR images are combined to several groups which include two correlative DR images. Image processing methods are used so as to get the centroid of each projection of the ball object at different position and then to construct an over-determined equation set. By solving the over-determined equation set, the X-ray focus projection coordinates are finally obtained. The experimental results prove that the improved method is free of the severe requirements of the elliptical projection shape according to the existing method, and the accuracy of this method can satisfy the requirements of the practical scanning systems, meanwhile it is easy to realize and of high anti-noise ability.