A data generating method includes: an atomic model generating step of generating one or more three-dimensional atomic models corresponding to a nanomaterial to be measured; a three-dimensional data generating step of generating three-dimensional atomic level structure volume data corresponding to the nanomaterial to be measured based on the one or more three-dimensional atomic model; a tilt series generating step of generating a tilt series by simulating three-dimensional tomography for a plurality of different angles in a predetermined angle range for at least some of the three-dimensional atomic level structure volume data; and a three-dimensional atomic structure tomogram volume data generating step of generating a three-dimensional atomic structure tomogram volume data set by performing three-dimensional reconstruction on at least some of the three-dimensional atomic level structure volume data based on the tilt series.