Provided are a file mutation method and a system using file section information and mutation rules. The file mutation system includes: a file section information extraction module obtaining file section information with respect to a sample file of a known file format; a file section information production module producing file section information with respect to a sample file of an unknown format; a mutation rule production module receiving a user input that a mutation rule is applied and producing a mutation rule, the mutation rule defining a mutation function that is to be applied to each data type; and a file mutation module receiving the sample file and producing a plurality of test case files that are created by mutating the sample file through the file section information processed in the file section information extraction module and the file section information production module and the mutation rule from the mutation rule production module.