A measurement-device-independent quantum key distribution (MDI-QKD) method with an air-water channel is researched. In this method, the underwater vehicle and satellite are the legitimate parties, and the third party is at the airwater interface in order to simplify the unilateral quantum channel to water or air. Considering the condition that both unilateral transmission distance and transmission loss coefficient are unequal, a perfect model of the asymmetric channel is built. The influence of asymmetric channel on system loss tolerance and secure transmission distance is analyzed. The simulation results show that with the increase of the channel’s asymmetric degree, the system loss tolerance will descend, one transmission distance will be reduced while the other will be increased. When the asymmetric coefficient of channel is between 0.068 and 0.171, MDI-QKD can satisfy the demand of QKD with an air-water channel, namely the underwater transmission distance and atmospheric transmission distance are not less than 60 m and 12 km, respectively.