I have an existing standalone SCCM 2012 hierarchy on a physical server with ~ 50K clients reporting with additional servers hosting various site system roles. Now the requirement is to migrate this hierarchy on a virtual environment. Client doesn't want to do P2V migration and wanted to have the migration done on new infra.

In current hierarchy we have client health compliance at ~90% and we have to maintain the same post migration additionally there are lot of collections, packages and deployments those needs to be successfully migrated.

Please suggest a feasible and most efficient solution for this

High level steps: take a backup of the existing server (CM / SQL, sources etc.), shut it down, bring up a new VM with the same (!) name, domain membership and disk layout and restore ConfigMgr. 
In case you can't use the same hostname (which makes things much more complicated then): install a new CM site using a different site and use CM's migration functionality to migrate all objects to the new site. Re-assign all clients. (Might not work when using the Intune

Also note that for an infrastructure of 50K clients, the hardware requirements are pretty significant. Using a VM for this on any type of shared infrastructure will most likely suffer performance wise. This is a huge consideration and should not b taken lightly. Make sure that the new VMs are on dedicated hosts with dedicated storage IOPS

Torsten,

In scenario 2 as per your response wherein I have to create a new SCCM 2012 hierarchy with a different Site code and Site server does the object migration works from one SCCM 2012 to another SCCM 2012. If Yes, what complications I can expect because of different site codes.

Thanks in Advance

Harsh

It also works from CM12 to CM12. Complications? Well ... reassigning all clients which will result in heavy load on the site server etc.

Client doesn't want to do P2V migration

Assuming that you have done your homework and are OK that Virtual is the way to go, the easiest way to migrate from Physical to Virtual is to carry out a P2V migration. I don't quite understand this.

Is there a checklist available which I can follow before actual migration.

Thanks in Advance

Have you been able to perform the migration? If so, could you enlighten me on the method you used? I'm looking at a similar situation where naming conventions make a difference between physical or virtual machines, so re-using the name of the current physical machine is not an option.