A memory storage device, a memory controller, and a virus scanning method are provided. In the method, a virus signature database recording a predetermined file segment and a corresponding virus signature is provided. A plurality of logical addresses is mapped to a part of a plurality of physical addresses in a rewritable non-volatile memory chip of the memory storage device, a host system accesses the logical addresses by using a file system including a file allocation table (FAT). At lease one binary code is received. The FAT is analyzed to identify a file segment containing the at least one binary code. If the file segment matches the predetermined file segment, the at least one binary code is not written into the memory storage device or transmitted back to the host system when the at least one binary code matches the virus signature corresponding to the predetermined file segment.