A write timeout control method for a flash memory having a plurality of spare blocks and data blocks including a plurality of mother blocks is disclosed. The method includes the steps of: receiving a write command and a starting logical block address; determining an update mode according to a target mother block linked to the starting logical block address; determining whether a pre-clean operation is performed on a first mother block; if so, performing a post-clean operation on the first mother block during a first time period; re-configuring the first mother block as a spare block; performing a programming process to write data on the target mother block; determining whether the number of mother blocks exceeds a first threshold; and if so, performing the pre-clean operation on a second mother block. The first and second mother blocks are configured as blocks to be cleaned.