A parallel data processing system based on location control and a method thereof can divide a data into smaller data and store and manage the divided data using a location control technique which divides a file, distributes the divided files, and stores and manages information on corresponding areas. The parallel data processing system includes an encryption and decryption server, a location control server and a storage device. Further, the system may reduce the time required for storing and reading a data and improve the speed of controlling encryption and decryption of the data as a result, by distributing the data in a plurality of storage devices and processing the data in parallel in encrypting, storing and restoring a data which requires security. In addition, performance of a plurality of storage devices and efficiency of the storage may be enhanced.