Hepatocellular carcinoma (HCC) is the third most common cause of mortality due to malignancy next to gastric cancer and esophageal cancer. Several causal factors have been proposed to be involved in the pathogenesis of HCC including regional and age difference, hepatitis virus, aflatoxin, chemicals, liver cirrhosis, and family heredity. Compared to the initial symptoms of HCC, the late symptoms are more obvious, which are liver pain, fatigue, emaciation, jaundice, and ascites. This paper summarized 30 biomarkers from organs, tissues, cells, and subcellular systems to be used for the diagnosis, detection, staging, and evaluation of the HCC so as to predict or prognoses diseases. The biomarker degrees of healthy people have a certain range of indicators. Pathological and clinical diagnostic methods are mainly used to detect various biomarkers related to HCC, such as the common detection of alpha-fetoprotein to detect HCC. Diverse indicators are determined by the modern technology so that we can explore and clarify the possible indicators associated with the pathogenesis of diseases in the organisms. In general, if one or more biomarkers are beyond the normal range, it would predict the presence of HCC in the body. Here, we try to provide a significant contribution toward clinical screening, prediction, diagnosis, treatment, and follow-up monitoring of HCC and related diseases through elucidating the conception, production and influencing factors, sources, and biochemical indicator-associated tumor markers.