Abstract: to study mechanism of relationship HBV gene mutation in chronic hepatitis B patients with TCM syndrome.HBV gene mutation along different types of TCM syndrome are detected by microarray assay.The rate of mutation of different sites are related to the type of TCM syndrome, Yin deficiency of liver and kidney 1764 (38%) , 1896 (68%) , 1899 (38%) ;collateral obstruction by blood stasis1762 (93%) , 1764 (90%) , 1899 (50%) .There are remarkable difference along the expression level of variant types of different TCM syndrome.1762、1764:collateral obstruction by blood stasis syndrome>Yin deficiency of liver and kidney syndrome>liver stagnation and spleen deficiency syndrome;1862: Yin deficiency of liver and kidney syndrome>liver stagnation and spleen deficiency syndrome;1896:Yin deficiency of liver and kidney syndrome>collateral obstruction by blood stasis syndrome>damp-heat blockage syndrome>liver stagnation and spleen deficiency syndrome;1899: collateral obstruction by blood stasis syndrome>Yin deficiency of liver and kidney syndrome>damp-heat blockage syndrome>liver stagnation and spleen deficiency syndrome.HBV gene mutation are related to TCM syndrome.The research has settled a basic technique for syndrome differentiation in molecule level.