A method of storing a pattern matching policy and a method of controlling an alert message are provided. The method includes (a) generating a content structure as a sub-structure of a header combination structure of a stored traffic pattern which is a policy to be newly applied to a pattern matching apparatus; (b) determining whether a content of the stored traffic pattern is identical to a content of an original traffic pattern stored in advance in the pattern matching apparatus; (c) allocating a content index of the content of the original traffic pattern to the content of the stored traffic pattern if the content of the stored traffic pattern is identical to the content of the original traffic pattern; and (d) determining whether a header combination structure of the original traffic pattern comprises only one content structure or more than one content structure and allocating a header index of the header combination structure of the stored traffic pattern to the header combination structure of the original traffic pattern if the header combination structure of the original traffic pattern is found to comprise only one content structure. Accordingly, it is possible to efficiently use hardware memories with limited storage capacities and effectively perform a pattern matching function.