A flash memory storage system having a flash memory controller and a flash memory chip is provided. The flash memory controller configures a second physical unit of the flash memory chip as a midway cache physical unit corresponding to a first physical unit and temporarily stores first data corresponding to a first host write command and second data corresponding to a second host write command in the midway cache physical unit, wherein the first and second data corresponding to slow physical addresses of the first physical unit. Then, the flash memory controller synchronously copies the first and second data from the midway cache physical unit into the first physical unit, thereby shortening time for writing data into the flash memory chip.