The invention relates to a method and an apparatus for cooling a multi-atmosphere segment continuous annealing furnace, the method comprises the following steps: hydrogen content in atmosphere of each furnace can be displaced to less than 1% through hydrogen displacement by nitrogen, a first seal curtain of an isolation segment of the furnace close to inlet of an annealing furnace is completely pressed, a second seal curtain is completely opened, opening degree value of a baffle plate of an exhaust uptake is set as 100%, atmosphere fluidity during subsequent blowing and cooling processes can be ensured; blowing and cooling by segment in each furnace can be carried out, when the temperature is reduced to 300 DEG C, a fire door of each segment is opened for air cooling and natural cooling. During the blowing and cooling processes in a dry/moisture atmosphere furnace, by setting the open and close mode of two seal curtains in each isolation segment and opening degree of the baffle plate, blowing and cooling can be completely and individually carried out in each furnace, problem of unsmooth air-exchange cooling due to long furnace length of the horizontal annealing furnace can be avoided, blowing atmosphere fluidity can be fully ensured, and cooling work efficiency is increased.