The invention provides a cleaning system and method for an alkali-associated carbonation tower, which aim to solve the problems of poor effect and low scar dissolving capacity in cleaning of the alkali-associated carbonation tower in the prior art. The cleaning system comprises cleaning agent storage equipment and cleaning gas conveying equipment, wherein the cleaning agent storage equipment is respectively connected with the upper part and the lower part of the alkali-associated carbonation tower, which meets a cleaning requirement, by a pipeline and used for storing ammonia mother solution I at a preset temperature; and the cleaning gas conveying equipment is connected with the lower part of the alkali-associated carbonation tower and used for feeding cleaning gas into the alkali-associated carbonation tower. The cleaning system and method with the technical scheme provided by the invention are beneficial to improving the scar dissolving capacity and the cleaning effect, and can prolong the working cycle of the alkali-associated carbonation tower, obviously improve the system productivity and save the production cost.