The invention discloses a method for inspecting deep packets based on a suffix automaton regular engine structure. The method comprises the following steps: S1, intruding an inspection system, extracting attack features and constructing regular expression, S2, constructing suffix nondeterministic finite automaton (NFA) engine and utilizing the suffix NFA engine to conduct multiple-pattern matching, S3, obtaining application layer protocol data packets and Web server log files from a Web server, S4, conducting deep packet inspecting on the protocol data packets and the log files and sending inspecting results to a firewall. According to the method for inspecting the deep packets based on the suffix automaton regular engine structure, matching of the multiple regular expression of a deterministic finite automaton (DFA) can be achieved by using a single automaton in a NFA mode, the problems that the NFA can not achieve the matching of the multiple regular expression and space explosion occurs when the DFA achieves the matching of the multiple regular expression are solved, the space size of the NFA is effectively reduced, the problems that a traditional NFA engine constructing method is waste in space and invalid traversal exists in the process of executing mode matching are solved, response time of deep packet inspecting is effectively shortened, and whole performance and efficiency of a system are improved.