A molecule design support apparatus has an input part, a display to display on a screen thereof a three-dimensional molecular structure by a half vector format or a ball-and-stick format, and a determining part to determine, in the molecular structure, an end that is to become a target of a coordinate modification with respect to a molecule in its entirety, in response to a bond axis of the molecule specified from the input part. The apparatus further has a modifying part to make a modification of the molecular structure based on the specified bond axis and the end that is the target of the coordinate modification, in response to the modification specified from the input part, and a display part to display a modified molecular structure on the screen of the display based on a determination made by the determining part and the modification made by the modifying part.