The aim of this study was to investigate the pathomorphological changes of chronic hepatitis B virus (HBV) infection and the coincidence between clinical and pathological diagnosis. Hematoxylin and eosin staining and immunohistochemistry for HBsAg and HBcAg were performed on 97 liver biopsy specimens collected from 97 patients with chronic HBV infection, including 55 HBV carriers. The agreement between clinical diagnosis and pathological diagnosis in mild, moderate and severe chronic hepatitis was 71.4, 60 and 83.3%. The rate of clinical diagnosis matching the pathological diagnosis for fibrosis was higher than for inflammation (83.33 vs 54.76%), especially in moderate (83.33 vs 26.67%) and severe chronic hepatitis (66.67 vs 16.67%). The rate of serological/imaging examination results and immunohistochemistry confirmation was as high as 93.81% for HBsAg and 92.78% for HBcAg. In HBV carriers, the degree of inflammation and fibrosis in most cases was mild, and the younger the patients, the higher the ratios of G0 and S0. The clinical diagnosis was correct in most cases, especially for inflammation and in mild chronic hepatitis; the patients who were diagnosed as HBV carriers actually already had inflammation and fibrosis.