This is the first time to solve the 3D frame structure with limited sensors by using the improved DSC method. The stiffness variation index (SVI) adopted is better than most others. The present results were compared against with the vibration data and damage history observed of a 12-story RC frame model under shaking table test of 62 scenarios, and was shown to be consistent. Both the full 3D finite element model and simplified cantilever model were used in the simulation.