1. An image processing system, comprising: an image processing apparatus including a scanner configured to read a first side of each of a plurality of documents and a second side of each of the plurality of documents after the plurality of documents are turned over so that positions of the plurality of documents when the second side faces up substantially coincide with positions of the plurality of documents when the first side faces up; and generate a first scanning image including first document images of the first side of the plurality of documents and a second scanned image including second document images of the second side of the plurality of documents; and a server including a memory and a processor, the processor configured to extract each of the first and second document images included in the first scanned image and the second scanned image; and register the first and second document images in the memory, wherein the first and second document images have a pair relationship based on relative positions of the first document images when the first side of each of the documents are read and the second document images when the second side of each of the documents are read.