As a new molecular marker, free DNA (cell free DNA, cfDNA) plays an increasingly important role in disease prediction, tumor prevention and treatment. However, there are still many obstacles before achieving a wide range of clinical application, mainly due to the lack of cfDNA-related standards, resulting in the lack of comparability of current research reports and the lack of stable repeatability of test results, thus reducing the reliability of clinical application. This review focuses on the related research progress of cfDNA in recent years, including sample source, sample preservation, sample extraction, qualitative and quantitative detection and application of cfDNA. We analyze and compare the various methods used in each link of cfDNA research and their advantages and disadvantages, analyze and summarize the problems existing in each link, and put forward the urgency of the formulation of cfDNA related standards.