Source: How to compact VirtualBox’s VDI file size?
You have to do the following steps:
1. Run defrag in the guest (Windows only)
2. Nullify free space:
With a Linux Guest run this:
dd if=/dev/zero of=/var/tmp/bigemptyfile bs=4096k ; rm -f /var/tmp/bigemptyfile
Or:
telinit 1 mount -o remount,ro /dev/sda1 zerofree -v /dev/sda1
With a Windows Guest, download SDelete from Sysinternals and run this:
sdelete.exe c: -z
(replace C: with the drive letter of the VDI)
3. Shutdown the guest VM
4. Now run VBoxManage’s modifymedium command with the --compact option:
With a Linux Host run this:
vboxmanage modifymedium --compact /path/to/thedisk.vdi
With a Windows Host run this:
VBoxManage.exe modifymedium --compact c:\path\to\thedisk.vdi
With a Mac Host run this:
VBoxManage modifymedium --compact /path/to/thedisk.vdi
This reduces the vdi size.