A molecular beam epitaxy apparatus comprises a growth chamber provided therein with a holder support frame and connected via a first gate valve to a preparation chamber which in turn is connected to a loading chamber via a second gate valve. A first transfer tray arranged in the loading chamber receives a set of substrates from outside and advances into the preparation chamber. A second transfer tray supports a substrate holder in the preparation chamber to allow the set of substrates to be transferred from the first tray onto the holder by the aid of a substrate transfer assembly. The second tray is advanced into the growth chamber to transfer the loaded holder onto the holder support frame.