This paper proposes a discrete-time overlapping decentralized guaranteed cost control algorithm via state feedback. Based on the inclusion principle, a structure system is decoupled into multiple subsystems, and the discretized subsystems’ controllers are designed by using the guaranteed cost control algorithm. Finally, the subsystems’ controllers are contracted into overlapping controllers of the original system, and the design of the control system is completed. This control method is introduced to the civil engineering field to solve the seismic control problem for discrete-time systems of building structures with uncertain parameters. The numerical analysis of the nine-story building structure model with uncertain parameters is carried out. The results show that the proposed control method can still effectively reduce the seismic response of discrete-time system when the structural parameters are uncertain, and the control effect is similar to the centralized control strategy; at the same time, the sampling rate and data transmission speed of the system are improved to ensure the reliability of the system. It illustrates the feasibility and effectiveness of the presented approach.