I want to set mongodb replication architecture like the following. My own server as the primary replica set and mongodb atlas as the secondary replica set. Can this be done? replication architecture
No you cannot. Please read the rest of the documentation (the picture of which you annotated) in https://docs.mongodb.com/manual/replication/ to fully understand how MongoDB replication works.
MongoDB Atlas is a Database-as-a-service, which runs self-contained MongoDB replica set. I believe what you are trying to do basically requires you to implement your own replication protocol.