I have a 10M folders. Each folder contains 13 files.
All these folders I would like to put in one main folder (root).
Is there any limitation in Windows Server for that?
As far the theoretical capacities of NTFS are concerned, there is no problem.
The Microsoft article on
Maximum Sizes on an NTFS Volume
specifies that the maximum of files per volume is 4,294,967,295,
and that should also be the maximum on folders.
However, you would need an extremely fast computer with lots of RAM to be able
to even view that folder in Explorer.
From my own experience, on a good computer of several years ago, viewing a folder
with thousands of sub-folders took some dozen of seconds just to show the folder.
I have no idea what would happen with 10 million sub-folders, but surely you
would need a lot of patience even if the computer could handle it. Eventually.
I really suggest to rethink again your folder architecture.