The present invention discloses a base coordinate system calibration method of an aircraft panel horizontal automatic drill riveter. The method comprises the following steps: 1) setting dead center positions of a rammer tight side machine tool and a drilling sprigging side machine tool in the aircraft panel horizontal automatic drill riveter, and drawing a coordinate system definition diagram; 2) respectively installing reflectors for measurement of a laser tracker at the machine tools at two sides of the aircraft panel horizontal automatic drill riveter, and appropriately arranging the laser tracker; 3) controlling translational shafts of two numerical control positioning devices in the aircraft panel horizontal automatic drill riveter to move to assigned positions in order, obtaining position coordinates of the reflectors on the two devices through tracking measurement of the laser tracker, fitting a straight line to express as the coordinate axis direction of each numerical control positioning device base coordinate system, and establishing the real positioning pose model of the base coordinate systems of the two numerical control positioning devices; 4) calculating the rotation matrix and the translation matrix from the base coordinate systems of the two numerical control positioning devices to a measurement coordinate system, and obtaining relative pose transformation matrixes R and T between the base coordinate systems of the two numerical control positioning devices.