Primary biliary cirrhosis (PBC) is an autoimmune liver disease characterized by the destruction of small intrahepatic bile ducts. Incomprehensible and complicated autoreactive responses participate in the development and progression of PBC, which involve various immune cells and inflammatory mediators. Based on the aspects of innate immunity and adaptive immunity, this article summarizes recent advances in the research on PBC pathogenesis at cellular and molecular levels and evaluates the clinical application of these studies. This article not only gives a feasible direction for researchers and clinicians in this study field, but also provides a theoretical basis for clinical diagnosis and novel therapeutic strategies.