A flash memory control method, a flash memory storage device and a flash memory controller are provided. The method includes the following. A flash memory module is instructed to perform a data merge operation to copy first data in a first physical unit into at least one second physical unit. After the first data is copied and before the first physical unit is erased, another programming operation is performed on the first physical unit to change a data storage state of at least a part of memory cells in the first physical unit from a first state into a second state. After the first physical unit is programmed, an erase operation is performed on the first physical unit.