A memory storage apparatus, a memory controller and method for transmitting and identifying data streams are provided. The memory controller passes at least a portion of a data stream received from a host system to a smart card chip of the memory storage apparatus. Then, the host system accurately receives a response message from the smart card chip by executing a plurality of read commands. The memory controller is capable of adding a first verification code to a response data stream sent to the host system, and is capable of adding a write token to each of data segments of the response data stream. The host system confirms the accuracy of the response data stream by verifying the first verification code or by verifying the write token of each of the data segments.