Provided are an anti-malware scanning system and a method thereof. The system includes: a host; and a chip which is removably connected to the host, receives a file to be scanned from the host, and scans whether malware exists in the file, wherein the host adjusts a size of the file to be scanned to correspond to a storage capacity of a storage unit of the chip and transmits the adjusted file to the chip. Accordingly, scanning is performed effectively even in an environment in which resources of the anti-malware scanning system are limited.