An X-ray inspection apparatus includes a 3D processing unit that performs 3D imaging of a first area in an inspection area, a 2D processing unit that performs 2D imaging of a second area in the inspection area, an extraction unit that extracts 3D information for a first inspection target from a 3D image of the first area, and 2D information for a second inspection target from a 2D image of the second area, a 3D information estimation unit that estimates 3D information for the second inspection target using the extracted 3D information for the first inspection target, and an inspection unit that inspects the second inspection target using the 2D information for the second inspection target and the estimated 3D information for the second inspection target.