A method, system, and article of manufacture tangibly embodying computer readable instructions for performing defragment on a physical hard disk of a host machine system having a virtual machine (VM) system. The host machine system performs contiguous storage of each file on the VM and the host machine with only one defragment. The host machine obtains a physical position distribution of data blocks in the hard disk constituting a VM file in the VM system according to VM file allocation information of the VM system and the host machine system file allocation information.