The present invention relates to an FK506 derivative which has reduced immunosuppressive activity but maintains nerve regeneration activity, a preparing method thereof, and a pharmaceutical composition comprising the same for preventing or treating nervous system diseases. A composition comprising 9-deoxo-prolyl-FK506, 31- O -demethyl-FK506, or 9-deoxo-31- O -demethyl-FK506 can promote nerve regeneration and has reduced immunosuppressive activity, thereby reducing side effects in the treatment of nervous system diseases.