Embodiments of the present invention provide a single photon based measurement device independent quantum communication system. The single photon based measurement device independent quantum communication system includes a transmitting end, a receiving end, and a third party; the transmitting end and the receiving end respectively prepare a first photo subsequence and a third photo subsequence forsecurity detection and send the first photo subsequence and the third photo subsequence to the third party for measurement, and then the transmitting end and the receiving end perform security detection according to the measurement result; after the security detection is passed, the transmitting end loads the information to be transmitted into a pre-constructed second photonic sequence, and transmits the information to the third party; the third party transmits a measurement result of the second photo subsequence to the receiving end so as to complete a communication process. The system can still achieve the absolute communication security guaranteed by the physical law while the measurement job is completely handed over to the third party, and ensures that only the receiving end can decode information transmitted by the transmitting end from information announced from the last third party.