synchronization works for messages in folder with this api
GET https://graph.microsoft.com/v1.0/me/mailFolders/{id}/messages/delta
we can get all messages in mailbox with this api
GET https://graph.microsoft.com/v1.0/me/messages/
Is there any way to synchronize messages in mailbox (as deltaLink in first api) irrespective of folders...
Not today. Delta queries are only specific to a folder, there's no Delta query that allows you to get all changes in all folders. You could request the feature on uservoice