The invention discloses a method for processing data on the basis of overlay file systems. The method includes steps of carrying out initial configuration on the basis of characteristics of the overlay file systems; executing corresponding operation according to different guide parameters to replicate and restore the data. The method has the advantages that file system structures are organized by the aid of the overlay file systems, core configuration data are sorted to confirm incremental replicated data and the restoration ranges, and the different guide parameters are designed to execute file replication and restoration operation; users only need to select different guide items, accordingly, the data can be quickly replicated and restored, the replication and restoration maintenance and service costs can be reduced to a great extent, and the accuracy of the replicated and restored data can be guaranteed. The invention further discloses a system for processing the data on the basis of the overlay file systems.