A memory controller is provided. The memory controller is coupled to a flash memory that includes a plurality of physical blocks, and each physical block includes a plurality of physical pages, and some of the physical pages are defective physical pages. The memory controller includes a processor that is configured to set a total target initialization time for an initialization process of the flash memory. The processor sequentially selects a current physical block from among all the physical blocks to perform the initialization process, and it performs a read operation of the initialization process on the current physical block using a read-operation threshold. In response to the read operation of the current physical block being completed, the processor dynamically adjusts the read-operation threshold of the read operation of the physical blocks, so that the initialization process is completed within the total target initialization time.