A method for performing Simple Storage Service (S3) seamless migration using index objects and associated apparatus are provided. The method includes: in response to a request of migrating user data of a user of the storage server from a remote S3-compatible server into the storage server, during an index stage, utilizing an index-object-based S3 migration management module among multiple program modules running on a host device within the storage server to create and store multiple index objects into a storage device layer of the storage server to be respective representatives of multiple normal objects of the user data at the storage server, and migrate respective Access Control Lists (ACLs) of the multiple normal objects to the storage server to be respective ACLs of the multiple index objects; and during a data stage, utilizing the index-object-based S3 migration management module to trigger one or more migration agents to migrate object data.