Hepatocellular carcinoma is serious harm to human health, and worldwide is one of the most common malignant tumors. Large study shows that caused by HBV hepatocellular carcinoma is about the proportion of global hepatocellular carcinoma of the 75 ~ 85% number, but the specific causes liver cancer HBV has not happening mechanism fully understood [1]. Recent research hepatitis b virus genotype, and various genotype HBV induced liver mechanism become a hotspot in current researches. Research shows that HBV genotypes may and disease process, after infection clinical manifestations, prognosis and antiviral treatment response, and so closely related. It is generally believed that caused genotype C inflammatory necrosis and fibrosis degree more serious than type B, and C and cirrhosis and HCC involved; The cumulative survival genotype B to significantly higher than C. Recent research shows that HBV mutation rate than other DNA about 10 times higher, HBV gene variants and the disease clinical outcomes related, mutant can cause pathogenic and copy ability increases, change the host immune response and the production of the important table bits of drug resistance to fight the virus. Because HBV different overlapping protein-coding genes, the promoter and enhance the son in such control sequence and within genes encoding, part of a gene mutation will affect many gene expression, thus forming a gene mutation [3] HBV, therefore, the more the comprehensive research of mutation of hepatitis b virus genome and biological significance especially important. In recent years the domestic and overseas scholars about HBV genotypes, variation of association with HCC relationship research done a lot of work, yunnan area in recent years have about HBV genotype distribution, but the reports of research on HBV genotypes, variation of association with HCC relationship research has not been seen reports. This study is to understand the yunnan region chronic HBV infection genotype infection situation, understand variation site testing conditions, the author discusses chronic HBV infection genotypes, common variation sites and hepatocellular carcinoma relationship.