A three-dimensional data generation device includes a data division unit, a detection unit, an output command unit, and a data correction unit. The data division unit divides sectional shape data on one layer of a shaped object into mark data for shaping a mark for correction of sectional shape data on a different layer to be output as superposed on the one layer and post-removal data obtained by removing the mark data from the sectional shape data on the one layer. The detection unit detects an amount of misregistration of the mark output using the mark data from a position determined in advance. The output command unit commands output using the post-removal data so as to form the one layer of the shaped object together with the mark. The data correction unit corrects the sectional shape data on the different layer using the amount of misregistration of the detected mark.