In this study, we reported the genome sequence of Burkholderia sp.CQ001, a Dexamethasone (DXM) degrading bacterium isolated from hospital wastewater and identified by morphological analysis, staining and 16S rRNA sequencing. The degradation rates of dexamethasone sodium phosphate and dexamethasone were 84.8% and 77.11% respectively. And degradation peak appeared at 24 h during agitation culture at 37°C in medium with an initial pH value of 7.5. Genome sequencing was performed using Illumina Hiseq4000 high-throughput sequencing platform. Genome sequencing results demonstrated that the bacteria had a total genome size of 7570308 bp, 66.9% G+C content. Metabolic related genes account for 80.3%. Metabolism-associated genes covered 116 metabolic pathways, including metabolic pathways of microorganisms in different environments and decomposition pathways of secondary metabolites. One of the eight key genes annotated to the metabolic pathway of steroid compounds. This is the first report on Burkholderia sp.CQ001 showing characteristics of degrading dexamethasone. Our findings may provide insights on dexamethasone degradation mechanisms, and facilitate the establishment of bioremediation engineered bacteria to eliminate the dexamethasone pollution.