High rise structures with strengthened stories are widely used nowadays. A rational seismic design procedure for this kind of structure is thus necessary. Based on mode theory and direct displacement based seismic design of multi-story buildings, this paper proposed a new direct displacement based seismic design procedure. In the proposed method, each mode of the high rise structure is equivalent to a single degree of freedom (SDOF) system. Seismic response of each mode is calculated and adds up to consider the contributions of higher modes. Considering the characteristic of strengthened stories, two stories above the strengthened stories are taken as the “key stories”, whose performance indicates the performance of the building. The proposed procedure is logical, simple and can serve for reference of actual design.