A writing method, a memory controller and a memory storage device are provided. The writing method includes steps of: configuring logical addresses to map to part of physical programming units in a storage area, wherein at least one of the physical programming units stores a valid data; transmitting a first write command for writing data having a first data length to at least one of the physical programming units; receiving a status signal; and selecting a spare physical erasing unit and copying the valid data having a second data length to the spare physical erasing unit, after transmitting the first write command and before receiving the status signal, wherein the first data length is not greater than the second data length. Therefore, it prevents a host system from waiting too long when writing data.