This paper proposes the fault detection and isolation (FDI) technique and presents the design method of FDI filter in active control system of structure based on H∞ robust control theory. The FDI system model is constructed according to H∞ object which changes the fault detection problem to a robust control problem. The H∞ optimal controller named FDI filter is worked out by linear matrix inequality (LMI). Simulation results for a three-story building demonstrated the effectiveness of FDI filter. This paper can provide a reference for the structure health monitoring of active control system and is the base of the fault tolerant control.