We have constructed an end station for nanoscale magnetic materials study at the soft X-ray beamline HiSOR BL-14 at Hiroshima Synchrotron Radiation Center. An ultrahigh-vacuum scanning tunneling microscope (STM) was installed for an in situ characterization of nanoscale magnetic materials in combination with soft X-ray magnetic circular dichroism (XMCD) spectroscopy experiment. The STM was connected to the XMCD experimental station via damper bellows to isolate it from environmental vibrations, thus achieving efficient spatial resolution for observing Si(111) surface at atomic resolution. We performed an in situ experiment with STM and XMCD spectroscopy on Co nanoclusters on an Au(111) surface and explored its practical application to investigate magnetic properties for well-characterized nanoscale magnetic materials.