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Vibration analysis is the great need and can be used in many practical applications, especially in monitoring the status of machines, bridges and other construction works. This paper presents a low-cost structural health monitoring scheme using MEMS-based accelerometers. The purpose of this scheme is to achieve the high performance system for bridge monitoring with low cost. The system can operate in two modes, real-time and offline. In the real-time mode, embedded real-time short-time Fourier transform programs on the 3-DOF accelerometers were performed for the monitoring and alert. In the offline mode, the analysis of bridge models was utilized based on DIAMOND tool for further analyses and evaluations. Initial results show that the system is suitable for practical applications.