The invention provides a protocol field reverse analysis system and method based on BWT. Specific suffix index is constructed, so that specific substring matching only needs to be completed once in each alignment process. Moreover, the alignment algorithm based on suffix index is flexible in design, consumes less space in the index stage, and the length of subsequence is variable, protocol fieldscan be quickly identified. After the fixed field is identified, the invention counts the fields with high frequency through a random multi-stream multi-segment matching method, constructs a grammar tree according to the field position and the number of the fields, extracts the field structure, and thus realizes the inverse of the field format. After being classified, the reverse field is used asthe input of the fuzzy test tool, a large number of deformity test cases is sent to the target communication entity, and at the same time, the debugger is combined with the sniffer to carry out abnormal monitoring on the target communication entity, the abnormality is found and analyzed, so as to subsequently improve the safety of the target communication entity.