Abstract: Accurate coordinate of X-ray source is one of the key parameters in design of micro CT based on cone-beam X-ray system. The method of calculating the coordinate of X-ray source through a metallic ball model's 2-D projections is represented. It is based on micro source system which the source is counted as a particle under a certain amplification. Coordinate of the source could be calculated through projective lines. Avoiding the micro CT system is fixed, cone-beam reconstruction formulas with a nonstationary shift of X-ray source are represented. Model test are performed to show the effect after corrected for the shift of X-ray source.