A multi-functional storage apparatus and a control method thereof for executing the steps of: receiving a first command outputted from an operation system through a driver and responding to the first command to make the operation system identify an attribute of the multi-functional storage apparatus; transferring an application program stored in a storage device of the multi-functional storage apparatus according to an executing request of the operation system; executing, by the operation system, the application program to generate a second command, wherein the first command and the second command pertain to a control transfer command (CTC) for enabling a control transfer; and receiving the second command to control a signal generator of the multi-functional storage apparatus to generate an external signal, transferring the external signal back to the operation system; and converting the CTC into a bulk transfer command (BTC) for enabling a bulk transfer.