A method for performing meta block management is provided. The method is applied to a controller of a Flash memory having multiple channels, where the Flash memory includes a plurality of blocks respectively corresponding to the channels. The method includes: utilizing a meta block mapping table to store block grouping relationships respectively corresponding to a plurality of meta blocks, where blocks in each meta block respectively correspond to the channels; and when it is detected that a specific block corresponding to a specific channel within a meta block does not have remaining space for programming, according to the meta block mapping table, utilizing at least one blank block corresponding to the specific channel within at least one other meta block as extension of the specific block, for use of further programming. An associated memory device and a controller thereof are also provided.