Hi @john john ,
Please refer to the following articles, first get all root folders from the library, and then cycle inside to change the user's permissions.
#Grant folder permissions to SharePoint Group
Set-PnPfolderPermission -List $ListName -identity $FolderServerRelativeURL -AddRole "Read" -Group "<group name>"
References to third-party article:
Set Folder Permissions using PowerShell
PowerShell to Get Folder Permissions
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