AbstractPrevious studies have shown that administration of antimetabolite methotrexate (MTX) caused a reduced trabecular bone volume and increased marrow adiposity (bone/fat switch), for which the underlying molecular mechanisms and recovery potential are unclear. Altered expression of microRNAs (miRNAs) has been shown to be associated with dysregulation of osteogenic and/or adipogenic differentiation by disrupting target gene expression. First, the current study confirmed the bone/fat switch following MTX treatment in precursor cell culture models in vitro. Then, using a rat intensive 5‐once daily MTX treatment model, this study aimed to identify miRNAs associated with bone damage and recovery (in a time course over Days 3, 6, 9, and 14 after the first MTX treatment). RNA isolated from bone samples of treated and control rats were subjected to miRNA array and reverse transcription‐polymerase chain reaction validation, which identified five upregulated miRNA candidates, namely, miR‐155‐5p, miR‐154‐5p, miR‐344g, miR‐6215, and miR‐6315. Target genes of these miRNAs were predicted using TargetScan and miRDB. Then, the protein‐protein network was established via STRING database, after which the miRNA‐key messenger RNA (mRNA) network was constructed by Cytoscape. Functional annotation and pathway enrichment analyses for miR‐6315 were performed by DAVID database. We found that TGF‐β signaling was the most significantly enriched pathway and subsequent dual‐luciferase assays suggested that Smad2 was the direct target of miR‐6315. Our current study showed that miR‐6315 might be a vital regulator involved in bone and marrow fat formation. Also, this study constructed a comprehensive miRNA–mRNA regulatory network, which may contribute to the pathogenesis/prognosis of MTX‐associated bone loss and bone marrow adiposity.