A method includes the steps of measuring a first transmitted wavefront in a first medium having a first refractive index and a second transmitted wavefront in a second medium having a second refractive index different from the first refractive index, and obtaining a refractive index distribution projected value of the object in each orientation by removing a shape component of the object utilizing measurement results of the first transmitted wavefront and the second transmitted wavefront and each transmitted wavefront of a reference object that has the same shape as that of the object and a specific refractive index distribution and is located in one of the first medium and the second medium with the same orientation as that of the object, and calculating a three-dimensional refractive index distribution of the object based on a plurality of refractive index distribution projected values corresponding to the plurality of orientations.