A two-dimensional nano-scale measuring system utilizing a two-dimensional combined optical and X-ray interferometer (2D COXI) was developed for the standardization of measurement in the nanometer region. The system consists of a 2D COXI and an atomic force microscope (AFM). The designed, two-dimensional, flexure-stage scans and the cantilever tip probes the nanostructure of the specimen. The calibrated optical interferometers in the 2D COXI were used to measure two-dimensional nano-scale lengths. The accuracy of the optical interferometers was enhanced to enable sub-nanometer measurements. To demonstrate the nano-scale measuring system, we used it to measure the nano-scale pitches of gratings.