Cell-free DNA (cfDNA) is the DNA fragment existing in human extracellular fluid. In specific physiological process (such as pregnancy) or pathological conditions (such as human malignancies), the contents of cfDNA in extracellular fluid will abnormally change. The contents and molecular characteristics of cfDNA make it have the potential as a kind of biomarker for diseases′ diagnosis. With the development of cfDNA detection technology such as sequencing and mass spectrometry, liquid biopsy based on cfDNA detection has been widely used in clinical tumor diagnosis, tumor treatment, prenatal examination, and research in autoimmune diseases. A systematic summary of the latest research progress in the development of cfDNA detection technology and the clinical application of liquid biopsy, as well as the research progress of cfDNA in the diagnosis and treatment of related diseases is summarized in this review.