A data writing method, and a flash storage system and a controller using the same are provided. The method includes grouping the physical blocks of a flash memory into the physical blocks of a data area, a spare area and a special area. The method also includes writing the update data into the corresponding physical block of the special area when the update data is the single accessing unit. The method may include moving a part of valid data in a physical block mapping a logical block where the update data is belonged into a physical block of the spare area during each data writing command. Accordingly, it is possible to reduce the response time for each data writing command, thereby preventing a time-out problem caused by a flash memory having a large erasing unit configured at the flash storage system.