The invention discloses a method for applying a modified epoxy anti-corrosion coating for lining segments. The method comprises the following steps: maintaining segments in maintenance water, taking out the segments from a maintenance pool, and placing in an outdoor fixed field with good ventilation; blending the anti-corrosion coating, cooling the coating with circulation water, and sequentially brushing the first coating and the finish coating on the segments by using a barrel; airing the coated segments for 3-4 hours, piling the segments into multiple stacks, wherein each stack comprises an upper layer, a middle layer and a lower layer, and square wood is arranged between every two vertically adjacent layers for padding, and transporting to construction sites to use later after the coating is completed. By adopting the method, the whole coating process can be completed by only moving and piling the lining segments once, so that the construction time is shortened, the labor and equipment are reduced, the land is saved as the lining segments are piled into three upper, middle and lower layers in a piling field, the coating efficiency of the lining segments is improved, the coating speed of the lining segments is remarkably increased as the barrel is adopted for coating, and the method is simple to operate, practical and reliable.