The invention discloses a back-end data processing system for a magnetometer device. The back-end data processing system comprises a data receiving and preprocessing module, an annular buffer module,a data curve drawing module, a magnetic field numerical value real-time display module and a data storage module, wherein the data receiving and preprocessing module is used for receiving and processing data collected by a magnetometer and storing the data into the annular buffer module; the annular buffer module is used for saving and providing data for other modules; the data curve drawing module is used for extracting a section of magnetic field data starting from the current moment to be drawn into a curve; the magnetic field numerical value real-time display module is used for extractingthe magnetic field value at the current moment from the annular buffer module and displaying the magnetic field value, and meanwhile, displaying the curve drawn by the data curve drawing module; and the data storage module is used for storing the data of the annular buffer module in an external memory in the form of a file. The back-end data processing system can be directly matched with a magnetometer acquisition system, and the storage of the data is completed; meanwhile, the magnetic field value is displayed; and the back-end data processing system is low in requirement on equipment performance and is particularly suitable for portable magnetometer equipment.