In order to further enhance the transmission distance and secret key rate of the Measurement-Device-Independent Quantum Key Distribution (MDI-QKD) system, the Pulse Position Modulation (PPM) technique is introduced to the MDI-QKD protocol, and a new efficient quantum key distribution protocol, named PPM-MDI-QKD protocol, is proposed by utilizing the empty pulses of the weak source and high dimensional encoding technology. In the protocol, two communication parties firstly construct a PPM frame consisting of M consecutive weak pulses, then combine the BB84 polarization encoding and PPM encoding schemes to operate high dimensional encoding, and finally sift out the secure key with the legal PPM frame, the successful Bell-state measurement results, and matched bases. The numerical results show that the PPM-MDI-QKD protocol outperforms MDI-QKD protocol when the intensity of signals is less than 0.13. Moreover, compared with 404 km, the longest distance reported so far, the transmission distance can theoretically be extended to 480 km and the key rate up to 5.4×10－4 bps in 404 km, with the same parameters.