In our previous study, we found that polymorphisms of the mpt64 gene in the Mycobacterium tuberculosis complex (MTBC) may be the reason for changes in the antigen produced, which may in turn cause alterations of related functions. Based on the data, we further analyzed T/B cell epitope regions and non-epitope regions and compared amino acid changes between them. It turned out the polymorphisms of MPT64 affected both T cell epitopes and B cell epitopes, which thus influenced cell-mediated immunity and humoral immunity at the same time. Both T cell epitope regions and B cell epitope regions had higher dN/dS values than corresponding non-epitope regions, which means the formers have accumulated significantly more amino acid changes than the latters.