A three-dimensional image reconstruction method of reconstructing a three-dimensional image of a specimen, the method comprising: attaching, on a surface of the specimen, a grid-like mark member in which rectangular openings are two-dimensionally arranged, alternately repeating a cross section preparation step and a sectional image acquisition step, the cross sectional preparation step comprising: disposing the grid-like mark member under a shielding member so that a side of each of the rectangular openings of the grid-like mark member forms a 45-degree angle with respect to a direction in which the linear end edge of the shielding member extends; a processing position determination step of adjusting relative positions of the shielding member and the grid-like mark member by using the grid-like mark member as an index of the processing position; and preparing a cross section of the specimen by using a sectional specimen preparation device which is provided with the shielding member disposed so as to cover a part of the specimen, and which prepares a cross section at a processing position on the specimen with an ion beam, the processing position being a boundary between a portion of the specimen exposed from a linear end edge of the shielding member and a portion of the specimen covered by the shielding member, the sectional image acquisition step comprising: acquiring a sectional image of the specimen with imaging means, and arranging a plurality of the acquired sectional images with an image processing device in the order in which the acquired sectional images have been captured. attaching, on a surface of the specimen, a grid-like mark member in which rectangular openings are two-dimensionally arranged, alternately repeating a cross section preparation step and a sectional image acquisition step, the cross sectional preparation step comprising: disposing the grid-like mark member under a shielding member so that a side of each of the rectangular openings of the grid-like mark member forms a 45-degree angle with respect to a direction in which the linear end edge of the shielding member extends; a processing position determination step of adjusting relative positions of the shielding member and the grid-like mark member by using the grid-like mark member as an index of the processing position; and preparing a cross section of the specimen by using a sectional specimen preparation device which is provided with the shielding member disposed so as to cover a part of the specimen, and which prepares a cross section at a processing position on the specimen with an ion beam, the processing position being a boundary between a portion of the specimen exposed from a linear end edge of the shielding member and a portion of the specimen covered by the shielding member, the sectional image acquisition step comprising: acquiring a sectional image of the specimen with imaging means, and the cross sectional preparation step comprising: disposing the grid-like mark member under a shielding member so that a side of each of the rectangular openings of the grid-like mark member forms a 45-degree angle with respect to a direction in which the linear end edge of the shielding member extends; a processing position determination step of adjusting relative positions of the shielding member and the grid-like mark member by using the grid-like mark member as an index of the processing position; and preparing a cross section of the specimen by using a sectional specimen preparation device which is provided with the shielding member disposed so as to cover a part of the specimen, and which prepares a cross section at a processing position on the specimen with an ion beam, the processing position being a boundary between a portion of the specimen exposed from a linear end edge of the shielding member and a portion of the specimen covered by the shielding member, disposing the grid-like mark member under a shielding member so that a side of each of the rectangular openings of the grid-like mark member forms a 45-degree angle with respect to a direction in which the linear end edge of the shielding member extends; a processing position determination step of adjusting relative positions of the shielding member and the grid-like mark member by using the grid-like mark member as an index of the processing position; and preparing a cross section of the specimen by using a sectional specimen preparation device which is provided with the shielding member disposed so as to cover a part of the specimen, and which prepares a cross section at a processing position on the specimen with an ion beam, the processing position being a boundary between a portion of the specimen exposed from a linear end edge of the shielding member and a portion of the specimen covered by the shielding member, the sectional image acquisition step comprising: acquiring a sectional image of the specimen with imaging means, and arranging a plurality of the acquired sectional images with an image processing device in the order in which the acquired sectional images have been captured.