Allogeneic hematopoietic stem cell transplantation (aHSCT) is the only curative option for many otherwise incurable diseases such as hematopoietic malignancies and genetic disorders. However, chronic Graft-Versus-Host Disease (cGVHD) is commonly seen in long-term survivors of aHSCT and has become the leading cause of non-relapse mortality. Little improvement has been made to the clinical management of cGVHD in several decades, which relies on systemic immunosuppression that is often associated with complications. This is expected to change with updated understanding of cGVHD pathogenesis brought by the development of several new murine models. It is broadly accepted that cGVHD development undergoes 3 biological phases: 1. Tissue damage and innate immune activation leading to donor T cells activation, 2. Compromised immune tolerance and disturbed immune reconstitution leading to autoimmunity, 3. Aberrant tissue repair and autoantibody deposition leading to activation of pro-fibrotic pathways. In this study, we sought to explore approaches to block cGVHD through the inhibition of each biological phase of cGVHD. First, we demonstrated that donor T cells allo responses is dependent on a Ca2+ dependent inositol trisphosphate 3-kinase B (Itpkb) – an enzyme downstream of T cell receptor activation and functions through regulation of intracellular Ca2+ level. Blocking Itpkb by genetic ablation or pharmacological inhibition completely blocked or attenuated cGVHD in 2 different cGVHD models with complementary clinical manifestations. Second, we demonstrated that the deregulated immune balance could be restored by infusion of a potent regulatory cell population, the invariant Nature Killer T cells (iNKTs). iNKT infusion expanded Treg population in a CXCR5 and IL-4 dependent manner and restored the T follicular helper/regulatory balance. Third, we demonstrated that pulmonary fibrosis as a result of end organ damage during cGVHD could be reversed by Pirfenidone, a drug approved by FDA for idiopathic pulmonary fibrosis. The effect was associated with reduced macrophage infiltration and TGF-β production. Finally, to identify cGVHD biomarkers for cGVHD early diagnosis and treatment, we conducted full spectrum proteomic analysis of serum samples from the well-established murine multi-organ system cGVHD model with bronchiolitis obliterans syndrome (BOS). Using high throughput, discovery-based Mass Spectrometry (MS) technique, we identified 4 potential biomarkers of cGVHD, of which CCL15 proved druggable and was verified in highly characterized and previously reported patient cohorts. Collectively, this work identifies several potential therapeutic targets and a verified biomarker that may improve cGVHD clinical management and diagnosis. In addition, this work provides new insights into cGVHD pathogenesis.