The invention discloses a method for handling a water burst in excavation of a subway inter-zone contact channel. The method includes the steps of firstly, leaking water drainage, wherein a concrete layer is sprayed to the top of the contact channel, drainage pipes and precipitation wells are arranged on the two sides of the contact channel, the water inlet ends of the drainage pipes are communicated with the interior of the contact channel, and the water outlet ends of the drainage pipes are communicated with the interiors of the precipitation wells; secondly, contact channel filling, whereinsandbags are stacked in the excavated contact channel and at the opening of the contact channel; thirdly, segment supporting, wherein steel tube inner supports are arranged in main tunnels at the twoends of the contact channel to support main tunnel segments; fourthly, ground and in-tunnel grouting, wherein on the ground, grouting reinforcement is carried out on soil around the contact channel and the main tunnels at the two ends of the contact channel with a ground sleeve valve tube grouting method, and in the main tunnels at the two ends of the contact channel, backfill grouting reinforcement is carried out on the main tunnel segments. The method can quickly and effectively complete the leaking water stopping work and guarantee smooth shield arrival.