The invention relates to a method for lifting a shipping caisson by a capsule trolley, which comprises the following steps: (1) taking the trolleys in place; prearranging two shipping rails on a shipping route of a shipping caisson and respectively arranging trolley groups on the shipping rails, wherein the trolley groups are not exposed out of the shipping rails at the moment; drawing the trolleys under the caisson to be shipped in place by a winding engine at the rear part of trolley seats; (2) lifting: injecting water into capsules of all trolley units of the trolley groups, lifting a caisson support plate on the capsules, leading the caisson support plate to be higher than the shipping rails and support the caisson; (3) shipping: after the caisson is supported, pushing the trolley units by a push device to travel on the rails to a preset semi-submerged position; and (4) unloading: after the caisson arrives in the appointed position, discharging the water of the capsules, leading the caisson to be positioned on a cushion beam for carrying a transport ship and finishing the whole lifting and shipping procedures. Compared with the traditional way, the method greatly reduces the requirement for the ground and is simpler and more convenient to operate.