Chronic graft-versus-host disease (cGVHD) involves immune and hematopoietic dysfunction and is a major complication associated with allogeneic hematopoietic stem cell transplantation. Cytopenia and bone marrow (BM) suppression often occur in cGVHD patients. The BM hematopoietic niche plays a central role in hematopoiesis. However, the effects of cGVHD on the BM hematopoietic niche and hematopoietic regulatory mechanisms remain unclear. To address these questions, we evaluated the hematopoietic, pathological and transcriptomic changes that occur in whole BM in a B6→C3H.SW minor mismatch murine cGVHD model. Pancytopenia and myelofibrosis developed in GVHD BM at day 40 post-transfer and were dependent on both CD4+ and CD8+ T cells. To clarify the molecular mechanisms underlying cGVHD-induced pancytopenia and myelofibrosis, we performed time-course transcriptome analysis of GVHD BM from the acute to chronic phases. By weighted co-expression network analysis-based clustering, we identified gene modules for which the expression kinetics was significantly correlated with changes in hematopoietic parameters and GVHD scores. Gene ontology analysis revealed that these gene modules contained larger numbers of fibrosis-related genes and serine/threonine kinase activity-related genes. Upstream analysis of these gene modules using GeneXplain software suggested a contribution of PDGFA, CTGF, NF-kb and STAT signaling in BM cGVHD progression. Consistent with this result, continuous inhibition of PDGF signaling by imatinib administration from day 13 post-transfer ameliorated cGVHD-induced myelofibrosis progression and upregulation of the expression of fibrosis-associated genes such as Col3 and Spp1 in the BM. However, this therapeutic intervention did not ameliorate cytopenia in cGVHD BM. Moreover, T cell depletion from day 13 post-transfer ameliorated cGVHD-induced myelofibrosis progression, but did not ameliorate cytopenia in cGVHD BM. Collectively, our data suggests that PDGF signaling regulates myelofibrosis progression in the chronic phase, but that the onset of BM cytopenia may occur in the acute phase of murine GVHD.