1. A reference coordinate calculating method for obtaining positions of a plurality of reference points arranged on a reference plate having a larger area than a measurement area of a measuring machine as coordinate points on a standardized reference coordinate system, the method comprising the steps of: a grouping step in which the reference points included in a measurable area of the measuring machine without a position of the measuring machine being moved are grouped as a group so that one of the groups in which the plurality of reference points are grouped shares at least three of the reference points with at least the other one of the groups; a measuring step in which the measuring machine measures the positions of the reference points for each of the groups; a reference point coordinate transformation function calculating step in which a reference point coordinate transformation function is calculated for each of the groups, the reference point coordinate transformation function respectively transforming the positions of the reference points which are shared by different groups and obtained by measuring the reference points in the different groups into the same or extremely approximate coordinate points; and a reference point coordinate transformation processing step in which coordinates of the positions of the reference points measured for each of the groups are transformed with the reference point coordinate transformation function calculated for each of the groups.