Provided are an apparatus and a method of managing a reconfiguration data memory. A space for a memory that stores configuration data used for reconfiguration of a target system is not provided in the target system. Instead the configuration data is stored in a separate server and, if required, the configuration data is transmitted to the target system through an Internet. Data that should be preserved after the reconfiguration among data contents stored in SoC internal and external memories of the target system is transferred to the server. The emptied space of the SoC internal and external memories is used as a configuration memory. After the reconfiguration, the preservation data is returned to its original position in the memories.