The invention provides a magnetic disk data backup system and a running method thereof. The system comprises a backup control device, a device for reading before writing, a backup reading device, a magnetic disk filter driving device, a page-change device, a backup snapshot table, a memory buffering queue and a hard disk buffering file. The system preferably gains the backup snapshot table which is used for recording whether the magnetic disk sector data requires backup or not; the magnetic disk sector data required for backup are sequentially read in the magnetic disk according to the gained backup snapshot table so as to carry out the backup, meanwhile, the operation of the magnetic disk started to be monitored; the write operation of the magnetic disk is monitored and intercepted; if the write operation signal is intercepted during the backup process, the data is read in the written magnetic disk and memorized to the memory buffering queue, and when the data of the memory buffering queue exceeds the pre-arranged length, the data is moved out to the hard disk buffering file, and a write operation allowance signal is sent so as to complete the operation of reading before writing. The system and the method of the invention can ensure the consistent time of the backup data, avoid the headlock under the situation that the upper-layer service is not interrupted, and has high service application independence.