A block management method applicable to a non-volatile memory storage system is provided. The non-volatile memory storage system includes a plurality of chips. Each chip includes a plurality of physical blocks. The physical blocks form a plurality of physical block sets. Each logical block in a logical space corresponds to at most two physical block sets. In the block management method, when a logical block corresponds to two physical block sets filled with data and more data is to be written, a free physical block set is allocated for storing the data. Then, one of the two physical block sets corresponding to the logical block is selected according to a predetermined criterion. The valid data in the selected physical block set is copied into the free physical block set. Next, the selected physical block set is erased and collected to the pool of free physical block sets.