Objective To study the quality control system for establishment of liver transplantation(LT)biological specimen (bio-specimens) bank for hepatocellular carcinoma(HCC), development of a standardized HCC for LT bio-specimens collection, processing and preservation operation process. To establish at sound and comprehensive information management system to conduct a systematic management of clinical information of collected specimens. Methods Referring to standardized procedures to establish bio-specimens banks, the operational processes system in HCC for LT sample collection and quality control system were developed and standardized. Liver tissue and blood samples of HCC patients for LT were collected, While liver tissue and blood samples of benign liver disease in liver transplant recipients and of healthy donor were collected as a research control. A systematic management of clinical information of specimens collected was conducted. Results From the development of standardized sample collection procedures, in August 2009, and from 501 recipients and donors for LT, specimens of tissues and blood samples were collected. The total number of HCC specimens including tumor tissues, adjacent tissues and remote non-cancerous tissue specimens was 1773. And 45 were randomly selected for DNA and RNA testing; the results proved that the accuracy rate of pathological sampling was above than 90% and these collected specimens had a high quality. HCC specimen information data computer management was established and improved. Conclusions The initial establishment of standardized research-based clinical transplantation specimens bank for HCC is helpful to improving the efficiency of sample collection and quality. It provides a standardized samples resources platform for scientific research in the field.