A dynamic hard disk mapping method and a server using the same are disclosed. The server includes a first motherboard, a second motherboard, a first disk group corresponding to the first motherboard, and a second disk group corresponding to the second motherboard. In the dynamic hard disk mapping method, at first, a disk redistributing instruction is received and stored. Thereafter, a reset instruction is received and performed. Then, the number of hard disks of the first disk group and the number of hard disks of the second disk group are summed up to obtain a total hard disk number N, wherein N is a positive integer greater than zero. Thereafter, the disk redistributing instruction is read, and a redistribution computation is performed in accordance with the disk redistributing instruction to obtain a third disk group corresponding to the first motherboard and a fourth disk group corresponding to the second motherboard.