The invention discloses a magnetic shielding protection body construction method for a magnetic navigation system operating room, which comprises the following steps of: site planning and examination; carrying out alignment to an operating room building, performing building positioning and setting and alignment on a magnetic shielding operating room according to a plane figure, a floor, a top surface, a wall magnetic shielding arrangement diagram and a detailed structure map in the magnetic navigation system operating room; and arranging inner and outer position lines of building retaining walls, X and Y centering axes, a control room, an operating room, equipment room wall position lines, regional axes, induction doors, a hand push door position line, electric slots and pipe laying channel lines of the magnetic navigation system operating room on the floor, wherein the requirements of the precision control are that the length-width error is controlled within 2mm, and the diagonal error is controlled within 4mm; mounting a ground component; mounting the magnetic navigation system; carrying out inspection and acceptance of the magnetic shielding; and the like. According to the operating room magnetic shielding protection body construction method, the health risk generated in the process of working around a magnet is reduced to the greatest degree, accidents are avoided, magnetic leakage is completely eliminated, and preventative measures are taken before the accidents occur.