In this study, it suggests new calibration method which calibrates x-ray imaging system. This method deals with calibration of geometries of x-ray instruments and calibration of image mapping parameters. It is devided into three calibration stages. At 1st stage, it is achieved to calibrate image mapping paremeters. At 2nd stage, dislocation of optical axis and axis of x-ray souce is adjusted. At 3rd stage, it calibrates total x-ray imaging system including xyz table. If we can calibrate all of stages, then, we'll get images with user-defined magnification. Paremeters that is obtained at each stage is optimized using steepest decent searching algorithm. So, more precise mappings is achieved. This method must be needed in automatic inspection system using x-ray instruments.