A block management method for a rewritable non-volatile memory module having a plurality of physical blocks, and a memory controller and memory storage apparatus using the same are provided. The method includes logically grouping the physical blocks at least into a data area, a free area and a replacement area and configuring a plurality of logical blocks for mapping to the physical blocks of the data area. The method also includes assigning bad physical blocks into the data area and marking the logical blocks mapping to the bad physical blocks as bad logical addresses, thereby forbidding the access of the logical blocks mapping to the bad physical blocks. According, the method can effectively use the rewritable non-volatile memory module having too many bad physical blocks to store data.