A controller capable of preventing spread of computer viruses is provided. The controller includes a microprocessor unit, and a first interface unit, a second interface unit, a comparing unit and a filter unit which are coupled to the microprocessor unit. The first interface unit is coupled to a storage medium, and the second interface unit is coupled to a computer host. The comparing unit determines whether data read form the storage medium by the computer host is an automatic executing file. And, the filter unit replaces the read data with a predetermined data and transmit the predetermined data to the computer host when the read data is the automatic executing file. Accordingly, the controller is capable of preventing the spread of the computer viruses designed in an automatic executing file.