A flash memory controlling apparatus includes a data read/write interface and a controller. The data read/write interface is arranged to couple a first flash memory and a second flash memory, wherein the first flash memory includes a first storage plane and a first buffer, and the second flash memory includes a second storage plane and a second buffer. When the read/write interface couples the first flash memory and the second flash memory, the controller is arranged to temporary store a plurality of valid data stored in the first storage plane into the second buffer. After an erase cycle is performed on the first storage plane, the controller further programs the plurality of valid data temporarily stored in the second buffer into the first storage plane.