A measuring point position automatic allocation method for a multi-head measuring apparatus is provided and includes steps as follows: obtaining point position coordinates for all point positions on a surface of a color filter that need measurement, grouping the point position coordinates, matching the Y-axis coordinates of each group with gantry mechanisms corresponding to a measuring range, according to the Y-axis coordinates of the gantry mechanisms matching X-axis coordinates with the measuring head mechanisms, sequentially matching the point position coordinates of all the point positions needing measurement with the gantry mechanisms and the measuring head mechanisms to complete allocation of the point positions.