Data accessing method for a flash memory, and a controller and a storage system using the same are provided. The data accessing method includes reading data from a physical address of a flash memory according to a physical address to be read corresponding to a logical address to be read in a read command, and determining whether or not the read physical address is the physical address to be read. The data accessing method also includes transmitting the data only if the read physical address is the physical address to be read. Accordingly, it is possible to ensure the transmitted data is data to be accessed by the read command.