Doping athletes tend to use new and non-approved drugs in an attempt to circumvent the dope test. Recently, a package of unknown drug was obtained from black market claiming to contain steroid-like compound, which could not be readily identified due to the lack of commercially available reference standards. In order to characterize and identify the chemical structure of the unknown compound, ultra performance liquid chromatography high resolution mass spectrometry (UPLC-HRMS), high performance liquid chromatography tandem quadrupole mass spectrometry (HPLC-MS/MS), gas chromatography tandem quadrupole mass spectrometry (GC–MS/MS) and nuclear magnetic resonance (NMR) instruments were applied in this work. Based on the combined data, the unknown compound was identified as 6β-chlorotestosterone. The aim of this study was to find urinary metabolic biomarkers of 6β-chlorotestosterone for clinical research and doping control analysis. Ten in-vivo metabolites including four phase I metabolites and six phase II metabolites were characterized and potentially identified. The detailed structure of the phase I metabolite was successfully obtained by GC–MS/MS analysis of trimethylsilylation (TMS) released upon dissolution, overcoming the absence of useful fragment ions to demonstrate the structure of sulfate metabolites. Two strategies including metabolic mechanisms and retention time variation of steroids were introduced to determine and distinguish 3α/β- and 5α/β- epimeric metabolites. A comprehensive evaluation was conducted on time of appearance and detection of each metabolite. The sulfate metabolite 6β-chloro-5β-androstan-17-one-3β-O-sulfate (S1) could be detected up to 12 days after oral administration, which was considered to be the long term biomarker for 6β-chlorotestosterone abuse in clinical research and doping control analysis.