The Exchange server is runninng on virtual machine.
Which method of backup is prefer for exchange Granular level recovery and which method is best practice
The backup of exchange server through agent based or
The Virtual machine backup with exchange application consistent enabled
Suggest some idea on this.
This is my view from inside Veritas, as one of the people who helps support engineers resolve customer issues.
There are reasons to prefer either way. Don't do both, because both methods truncate logs.
If you run a VMware policy without the Exchange option, and also back up Exchange with an Exchange policy, then you will back up the Exchange data twice. (An MS-Windows policy rather than a VMware policy excludes the Exchange data files.)
If you have a DAG, an Exchange policy can distribute the backup across the Exchange servers in the DAG. You can back up passive copies of some databases and active copies of others by designating which servers can be used for passive copies.
A VMware policy with the Exchange option catalogs the Exchange data for the databases that are active on each VM. The VM phase of the backup truncates logs for those databases.
Exchange GRT in a VMware backup requires that the NetBackup Framework Discovery service (nbdisco) on the VM has enumerated lists of mailboxes for each database in advance. In an Exchange policy backup, if the lists aren't already there, NetBackup creates them during snapshot processing.