Chronic graft versus host disease (cGVHD) is the major reason of late non-relapse related death after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The therapeutic regimen based on glucocorticoids remains as the standard initial treatment of cGVHD. But due to the significant side effects and unsatisfactory outcomes, particularly for patients with steroid-refractory disease, the more effective and less toxic therapies should be needed. Abnormal regulation for the stable state of T lymphocytes and B lymphocytes for allo-HSCT patients is the current focus of studying cGVHD pathogenesis. This article summarizes the treatment of cGVHD targeted to pathogenic factors and signaling pathways in pathogenetic process.