In the three-dimensional micro-computerized tomography scanning system, it is impossible to measure the positions of the X-ray focus and imaging plane of the detector by direct means. A simple and feasible method to measure the X-ray focus projection coordinates with high accuracy is proposed. This method is based on the theory that the projection of the sphere object in the cone-beam field is an ellipse. Through acquiring the digital radiography images of the double sphere objects, the image and graphics processing methods and the least square fitting method are used to get the intersection point of the major axis of the two ellipses. The intersection point is also the X-ray focus projection on imaging plane of the detector. The experimental results prove that the accuracy of this method can satisfy the requirements of the practical micro-comptuterized tomography scanning system, and is easy to realize with high anti-noise ability.