With recent trends of super-tallness, atypical plan shapes and zoning constructions in high-rise buildings, a structural stability of the building under construction is arising as a key issue for design and construction plan. To ensure the structural stability under construction, the differential column shortening of vertical members, the lateral displacement of tower frames, and differential settlement of raft foundation by unbalanced distributions of a tower self-weight before the completion of a lateral load resisting system should be checked by construction sequence analysis, which should be performed by systematic combinations with structural health monitoring, construction compensation program, and construction panning. This paper presents the scheme of zone-based construction sequence analysis by using the existing commercial analysis program, to check the stability of high-rise building under construction. This scheme is applied to 3-dimensional structural analysis for a real high-rise building under construction. The analysis includes real construction zoning plans and schedules as well as creep and shrinkage effects and time-dependent properties of concrete. The simplified construction sequence and assumed material properties were continuously updated with the change on construction schedule and correlations with in-situ measurement data.