In this paper, a smart wireless MEMS-based accelerometer(MA) system has been designed and experimented for smart monitoring system of civil structures. In order to estimate the performance of a smart wireless MA system(SWMAS), dynamic characteristics of our model structure need to be identified. This system thus employed a high-performance AVR microcontroller, a wireless modem, and MA for multiplex communication capability and real time duplex communication. Various performance and experimental tests have been carried out to evaluate whether this system is suitable for monitoring system of civil structures. First, we examined its sensitivity, resolution, and noise, specifically to evaluate the performance of the smart wireless MA system. The results of experiments enabled us to estimate performance of the MA in SWMAS in comparison to the value of data sheet from MA. Second, characteristics of model structure were analyzed by the ambient vibration test based on the NExT combined with ERA. Finally, this analysis was compared to the one that was made by FE results, and the comparison proved that a smart wireless MA system was fitted in smart monitoring system effectively.