A memory storage device, a memory controller thereof, and a method for automatically creating a fill-file thereof are provided. In the present method, a plurality of logical addresses is configured and grouped into a plurality of logical blocks to be mapped to physical blocks of a memory chip in the memory storage device. When a host system is powered on, whether the logical addresses have been formatted into a partition is determined. If the logical addresses have been formatted into a partition, whether a fill-file of a predetermined file capacity exists is determined. If the fill-file does not exist, data related to the fill-file is respectively filled into a file allocation table (FAT) and a root directory of the formatted partition when the host system reads the FAT and the root directory, so as to automatically create the fill-file.