A method for performing block management is provided. The method is applied to a controller of a Flash memory having multiple channels. The Flash memory includes a plurality of blocks respectively corresponding to the channels. The method includes: selecting at least one meta block having at least one valid page as at least one candidate meta block for being cleaned, and accumulating respective valid page counts of blocks respectively corresponding to the channels within the at least one candidate meta block, in order to generate a plurality of accumulated values respectively corresponding to the channels; and when it is detected that all of the accumulated values reach a threshold value, triggering a cleaning operation with regard to all candidate meta blocks, in order to simultaneously move/copy valid data respectively corresponding to the channels during the cleaning operation. An associated memory device and a controller thereof are also provided.