The invention discloses a backfill crossing method for a shield tunneling machine passing through a middle air shaft. The method comprises the following steps: 1) end reinforcing construction: the ends of a tunnel outlet end and a tunnel inlet end of the middle air shaft shield tunneling machine are reinforced; and a reinforcing end is positioned at the outer side of a middle air shaft surrounding ground connecting wall; 2) separation wall construction and tunnel door break construction: a separation wall is constructed between left and right two tunnels; the local part of the middle air shaft surrounding ground connecting all is broken to form a tunnel door for passing through the shield tunneling machine; a backfill area is formed; and a foam plate is arranged at the inner side of the backfill area; 3) backfill construction: mortar is filled back in the backfill area 6; and 4) after the strength of the filled mortar satisfies the tunneling requirements, the shield tunneling is performed, and the shield tunneling machine passes through the filled middle air shaft. The method adopts a proper backfill material to fill the middle air shaft, so that the shield tunneling machine directly crosses through the middle air shaft under the state of keeping continuous tunneling, and the starting and the reception of the shield tunneling machine in the middle air shaft can be prevented.