The present invention relates to a method and its system for calibrating measured data between different measuring tools. A method of calibrating measured data between different measuring tools includes the steps of: measuring the CD average dimension and roughness of an object to be measured using a CD-SEM tool; calculating the number of the cross section measurement points required for calibration by statistically processing the roughness; measuring the cross section of the object to be measured using the cross section measuring tool to satisfy the number of the cross section measurement points, thereby calculating the CD average dimension of the cross section measurement height specified in the obtained cross section measurement result; and calculating a calibration correction value being a difference between the CD average dimension of the object and the CD average dimension of the cross section measurement height of the object.