1. A three-dimensional structure verification supporting apparatus for supporting verification of an artificial three-dimensional structure by verifying properness of a three-dimensional simulated image simulated in order to indicate a three-dimensional structure of a substance, comprising: a first displaying unit for displaying an simulated three-dimensionally shaded model image assumingly indicating the three-dimensional structure of the substance by shading the three-dimensional simulated image; and a second displaying unit for displaying the three-dimensional image of the substance acquired by experimental structural analysis, wherein the simulated three-dimensionally shaded model image and the experimental image rotate synchronously.