A control method and an allocation structure for a flash memory device are provided herein. The flash memory device has a first memory module and a second memory module. Physical blocks of the first memory module and physical blocks of the second memory module are respectively divided into a plurality of groups, each of which has a plurality of the physical blocks. A first subunit and a second subunit of a first allocation unit are interleavingly written into a first group of the groups of the first memory module and a second group of the groups of the second memory chip respectively. Additionally, a first subunit and a second subunit of a second allocation unit are interleavingly written into a third group of the groups of the first memory module and the second group, respectively.