System and computer-implemented method for migrating partial tree structures of virtual disks for virtual computing instances between sites in a computer system uses a compressed trie, which is created from target tree structures of virtual disks at a plurality of target sites in the computer system. For a virtual computing instance selected, the compressed trie is used to find candidate target sites based on a disk chain string of the virtual computing instance. For each candidate target site, a cost value for migrating the virtual computing instance along with a partial source tree structure of virtual disks corresponding to the virtual computing instance from the source site to the candidate target site is calculated to select a target site with a lowest cost value as a migration option to reduce storage resource usage in the computer system.