The Structural Health Monitoring (SHM) systems monitor the condition of structures in order to promptly and quantitatively evaluate risks due to their deterioration or damage. The SHM systems require deployment of many sensors. However, it has been found that the management of the sensor network configuration and data transfer becomes extremely difficult when many kinds of sensors are used at once. In addition, for accurate diagnosis of a structure we need statistical information of similar and different structural systems. Thus we need standardized data structures for databases and the rules (protocols) for data transfer. Furthermore, using the databases, we can make the configuration control of sensor networks autonomous. For demonstrating the potential of the proposed database system, we selected the database system used XML. The metadata associated with acquired data and the sensor configuration are properly modeled and used for autonomous configuration control and data transfer.