A method, an apparatus and a controller for managing memories are provided. In the present invention, a data accessing format of each of the memories is adjusted such that the accessing units for each data accessing operation are unified. A mapping table is then established for recording the adjusted data accessing format. When a data accessing command is received from a host, the mapping table is inquired so as to execute the data accessing command. Accordingly, incompatibility of hardware structures can be resolved, and management of different types of flash memory can be achieved.