The invention relates to an anti-confusion system and a method for software virtual machine protection. After a program is traced and a tracing file is obtained, a heuristic analysis strategy is adopted to analyze a trace file to obtain a software virtual machine instruction set; then the semantics is extracted from the instruction set of the virtual machine; finally, anti-obfuscation is realizedby rewriting and optimizing compilation. The invention aims at the program protected by the commercial software virtual machine vmprotect, the instructions executed by the optimized program are reduced by 2/3 on average, and the program is easy to be modified, thus overcoming the defect of the prior software virtual machine reverse analysis method.