1. A system for guiding capsule medical device, comprising: a capsule medical device includes therein first and second imaging units that image images in imaging directions different from each other and a permanent magnet; a magnetic guidance device that applies a magnetic field to the permanent magnet to magnetically guide the capsule medical device in a subject; an operation input unit that receives operation information to operate magnetic guidance of the capsule medical device; a control device that controls the magnetic guidance device to magnetically guide the capsule medical device in response to the operation information input through the operation input unit; and an image display device that displays a first in-vivo image of the subject imaged by the first imaging unit and a second in-vivo image of the subject imaged by the second imaging unit, and clearly shows which of the first and second in-vivo images is an operation target image at the time of the magnetic guidance of the capsule medical device.