A method and system for configuring a multi-mode base station is disclosed so that a network system may specify a radio access mode for the base station. In the present invention, a configuration control unit inside the base station reports resource capabilities of the base station to a configuration decision unit. The configuration decision unit determines a mode for the base station according to network planning and the reported resource capabilities, generates a configuration file for the base station according to the determined mode, and delivers the configuration file to the base station. The configuration control unit configures relevant resources of the base station according to the received configuration file. The base station sends a configuration request during initial startup to implement automatic configuration. At daily startup, the base station reports resource capabilities and the existing configuration file to the configuration decision unit to check whether the current configurations are valid.