Objective To analyze the epitopes of cDNA sequences of Deinagkistrodon acutus snake venom metalloproteinases using bioinformatical method, and to observe the immune protective effect of the new immunogen designed according to the identified epitopes. Methods The cDNA sequences of Deinagkistrodon acutus snake venom metalloproteinases were amplified by PCR. The epitopes of the sequences were analyzed by Jameson-Wolf method and Clustal X software, then the sequences of the screened epitopes were artificially synthesized and linked to the vector pIRESneo. BALB/c mice were immunized by the resultant plasmid at 0, 2, and 4 weeks for three times, then the titers of the anti-serum were measured by ELISA. The immune protective effects of the anti-serum were tested by the neutralization of venom hemorrhagic activity and venom attacking test. Results Bioinformatical analysis yielded 6 epitopes (MPA-1-MPA-6). The ELISA results of anti-serum showed that these epitopes could induce immune reaction in mice, and the anti-serum was detectable even when it was diluted to 1100. The neutralization test and venom attacking test demonstrated that the anti-serum induced by the epitodes could neutralize the venom and protect the mice from haemorrhage. Conclusion Six epitopes of Deinagkistrodon acutus snake venom metalloproteinases have been obtained successfully using bioinformatical method, and the new immunogen designed based on these epitopes shows a primary immune protective effect.