The present invention relates to a compensation method for structural deformation occurring during construction of a super tall building, which includes the steps of: selecting horizontal and vertical members predicted to require compensation for horizontal and vertical deformation amounts; calculating deformation amounts based on the casting time of structural concrete for the selected horizontal or vertical members; determining compensation amounts based on the casting time of structural concrete for the selected horizontal or vertical members; calculating deformation amounts of the selected horizontal or vertical members up to and subsequent to the non-structural construction processes; determining compensation amounts by process of the selected horizontal or vertical members; and constructing the selected horizontal or vertical members by floors.