A method and apparatus for intelligent automatic reconfiguration of a network system basically implements an automatic reconfiguration apparatus to acquire the configuration of every network device and generates a topology of the network devices. Afterward, the automatic reconfiguration apparatus can detect the status of the network devices. When some network device is replaced by a new network device due to a breakdown or other factors, the automatic reconfiguration apparatus can detect the changed status and check the hardware version as well as the corresponding location in the topology of the former network device. If the hardware version of the new network device is identical to the hardware version of the corresponding former network device in the topology, the disclosed apparatus can automatically load the stored prime configuration into the new network device for performing automatic configuration to the network device.